feat(runtime): read-only accessors for the compiled identity, and use one

el_cgi_init loaded the declared identity into runtime globals and printed it, and
nothing read it back out. No accessor existed and it writes no state, so every
consumer still read identity from the mutable state store. studio.el's registry
read state_get("soul_principal") — a key with no producer anywhere — and reported
an empty principal under a heading reading 'Principal Covenant v1'.

Adds cgi_name/cgi_dharma_id/cgi_principal/cgi_network/cgi_engram. READ-ONLY on
purpose: there is deliberately no setter. Publishing these into the state store
would have been one line and would have recreated exactly the runtime-mutable copy
IDPROTO claims 1-2 forbid ('not modifiable by any runtime mechanism including
environment variables, configuration files, or API calls').

dharma_registry now reads the compiled constant. cgi_id keeps its state read
deliberately — the runtime instance id is a different fact from the compiled
dharma_id, and conflating them would hide a binary running under an id its own
declaration never claimed.

Measured, same corpus, binary the only variable:
  deployed engine  -> "principal":""
  accessor build   -> "principal":"william-christopher-anderson"
  interface: 110 routes in, 110 out, nothing removed

Requires the codegen fix in el (fix/cgi-identity-emission); without it the
declaration is never compiled in and the accessors return empty.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

.gitea/workflows/ci.yaml

@@ -34,12 +34,12 @@ jobs:
       - name: Install build dependencies
         run: |
           apt-get update -qq
-          apt-get install -y gcc libcurl4-openssl-dev apt-transport-https ca-certificates
+          apt-get install -y gcc curl libcurl4-openssl-dev apt-transport-https ca-certificates
           echo "deb [trusted=yes] https://packages.cloud.google.com/apt cloud-sdk main" \
             > /etc/apt/sources.list.d/google-cloud-sdk.list
           apt-get update -qq && apt-get install -y google-cloud-cli
 
-      - name: Download El runtime from Artifact Registry
+      - name: Authenticate to GCP + stage PINNED El runtime
         env:
           GCP_SA_KEY: ${{ secrets.GCP_SA_KEY }}
         run: |
@@ -47,41 +47,31 @@ jobs:
           gcloud auth activate-service-account --key-file=/tmp/gcp-key.json
           gcloud config set project neuron-785695
 
+          # PINNED RUNTIME — do NOT pull "latest" from Artifact Registry.
+          # The ship-soul calls engram_prune_telemetry (awareness.el sync/heartbeat
+          # self-review). The latest published el-runtime-c no longer defines that
+          # symbol, so an unpinned build fails to LINK — which is exactly how a
+          # broken/handlerless soul reached prod before. Compile against the
+          # vendored release runtime v1.0.0-20260501: the exact runtime the merged
+          # ship-soul was verified against (verify-soul-contract GATE PASS +
+          # genesis boot survives + full safety-contact response). It is committed
+          # under vendor/ so the soul build is fully reproducible and never depends
+          # on a moving AR "latest".
           rm -rf /opt/el/runtime
           mkdir -p /opt/el/runtime
+          cp vendor/el-runtime/v1.0.0-20260501/el_runtime.c /opt/el/runtime/el_runtime.c
+          cp vendor/el-runtime/v1.0.0-20260501/el_runtime.h /opt/el/runtime/el_runtime.h
+          echo "El runtime PINNED to v1.0.0-20260501: $(ls /opt/el/runtime/)"
 
-          # Get latest version of each runtime package (elc/elb not needed — we compile
-          # dist/soul.c directly; running elb on Linux OOM-kills the runner, and we
-          # always use the repo's pre-built soul.c anyway).
-          get_latest() {
-            gcloud artifacts versions list \
-              --repository=foundation-prod \
-              --location=us-central1 \
-              --project=neuron-785695 \
-              --package="$1" \
-              --sort-by="~createTime" \
-              --limit=1 \
-              --format="value(name)" 2>/dev/null | awk -F/ '{print $NF}'
-          }
-
-          RC_VER=$(get_latest el-runtime-c)
-          RH_VER=$(get_latest el-runtime-h)
-
-          echo "Downloading runtime@${RC_VER}"
-
-          gcloud artifacts generic download \
-            --repository=foundation-prod --location=us-central1 --project=neuron-785695 \
-            --package=el-runtime-c --version="${RC_VER}" \
-            --destination=/opt/el/runtime/
-
-          gcloud artifacts generic download \
-            --repository=foundation-prod --location=us-central1 --project=neuron-785695 \
-            --package=el-runtime-h --version="${RH_VER}" \
-            --destination=/opt/el/runtime/
-
-          mv /opt/el/runtime/el_runtime.c* /opt/el/runtime/el_runtime.c 2>/dev/null || true
-          mv /opt/el/runtime/el_runtime.h* /opt/el/runtime/el_runtime.h 2>/dev/null || true
-          echo "El runtime ready: $(ls /opt/el/runtime/)"
+      # neuron#133: CI compiles dist/soul.c, NOT the .el sources. On 2026-08-07 a
+      # build off main would have shipped an engine with none of five merged fixes,
+      # including a P0 safety fix, while main's source read as correct. The runner
+      # cannot regenerate the amalgam (elc needs 24GB+ virtual memory), but it can
+      # refuse to compile a stale one. Fails loudly with the recipe in the message.
+      - name: Verify dist/soul.c matches the sources
+        run: |
+          chmod +x tools/soulc-stamp.sh
+          ./tools/soulc-stamp.sh --check
 
       - name: Build neuron soul binary
         run: |
@@ -94,19 +84,37 @@ jobs:
           # entirely: elb on Linux would OOM the runner (elc uses 24GB+ virtual memory
           # on a 16GB host) and we always restore from the repo's soul.c anyway.
           mkdir -p dist
-          cc -O2 -DHAVE_CURL \
+          # -rdynamic: the el runtime resolves the HTTP request handler (and the
+          # tool handlers) by NAME via dlsym(RTLD_DEFAULT, "handle_request").
+          # macOS exports these symbols freely, but glibc/Linux only makes symbols
+          # visible to dlsym if they are in the dynamic symbol table — so without
+          # -rdynamic the stripped Linux binary boots but returns "el-runtime: no
+          # http handler registered" for EVERY route (i.e. a soul that serves
+          # nothing). Same reason the Windows build links -Wl,--export-all-symbols.
+          cc -O2 -DHAVE_CURL -rdynamic \
             -I$RUNTIME \
             dist/soul.c \
             $RUNTIME/el_runtime.c \
             -lssl -lcrypto -lcurl -lpthread -lm \
             -o dist/neuron
 
-          # Strip debug symbols and non-essential symbol table entries.
-          # -s removes the symbol table + relocation info (max size reduction).
-          # Keeps the binary functional; debuggability is preserved via source + CI logs.
+          # -s strips .symtab + debug for size. .dynsym (which -rdynamic populated
+          # with the dlsym-resolved handlers) is preserved, so the handler still
+          # resolves after stripping.
           strip -s dist/neuron
           ls -lh dist/neuron
 
+      - name: Soul contract gate (HARD BLOCK — no destructive/stale soul publishes)
+        run: |
+          # Boots dist/neuron on a throwaway port with a throwaway HOME/engram/cgi
+          # (never touches ~/.neuron or any live service) and fails the build if any
+          # app-contract route is unanswered (PRESENCE) or any engram write route
+          # hard-deletes instead of tombstoning/superseding (IMMUTABILITY). Non-zero
+          # here blocks Publish -> Artifact Registry -> GKE deploy, so a stale or
+          # memory-destroying soul can never reach prod.
+          chmod +x dist/neuron scripts/verify-soul-contract.sh
+          bash scripts/verify-soul-contract.sh dist/neuron 7796
+
       - name: Smoke test
         run: |
           file dist/neuron

awareness.el

@@ -889,10 +889,29 @@ fn awareness_run() -> Void {
             state_set("soul.last_beat_ts", int_to_str(now_ts))
             // Persist in-process Engram (sessions, memories, conversation nodes)
             // to local snapshot so they survive restarts.
+            // FILE MODE ONLY: "soul_snapshot_path" is set exclusively in the
+            // genesis+safe_to_seed branch of soul.el, and safe_to_seed is
+            // unconditionally false when ENGRAM_URL is set. In HTTP mode the
+            // owner persists; the soul must not (soul.el:571-573).
             let snap_path: String = state_get("soul_snapshot_path")
             if !str_eq(snap_path, "") {
                 mem_save(snap_path)
             }
+            // WRITE-THROUGH RETRY (neuron#117). The HTTP-mode counterpart of the
+            // save above: hand anything still spooled to the persistence owner.
+            //
+            // This is the retry arm of the whole design. Deltas that could not be
+            // pushed — owner down, owner restarting, transient refusal — stay on
+            // disk and are re-offered here every heartbeat until they land. It is
+            // also the catch-all for writes made by the awareness loop itself,
+            // which never passes through the HTTP handler's flush point.
+            //
+            // No-op with no HTTP call when the spool is empty or ENGRAM_URL is
+            // unset, so an idle soul in file mode pays nothing for this.
+            let wt_pushed: Int = wt_drain()
+            if wt_pushed < 0 {
+                ise_post("{\"event\":\"write_through_backlog\",\"ts\":" + int_to_str(now_ts) + "}")
+            }
         }
 
         // Curiosity scan: idle-gated AND wall-clock based. Only fires when the

chat.elh

@@ -1,4 +1,4 @@
-// auto-generated by elc --emit-header — do not edit
+// auto-generated by elc --emit-header - do not edit
 extern fn chat_default_model() -> String
 extern fn engram_numeric_valid(s: String) -> Bool
 extern fn parse_float_x100(s: String) -> Int
@@ -16,18 +16,35 @@ extern fn engram_nodes_merge(a: String, b: String) -> String
 extern fn id_in_seen(node_id: String, seen: String) -> Bool
 extern fn add_to_seen(seen: String, node_id: String) -> String
 extern fn engram_extract_ids(nodes_json: String) -> String
+extern fn affective_node_ts(node_json: String) -> Int
 extern fn engram_compile(intent: String) -> String
 extern fn distill_transcript(transcript: String) -> String
 extern fn json_safe(s: String) -> String
 extern fn current_engine_note(model: String) -> String
+extern fn bounded_persona_floor() -> String
+extern fn operator_identity_block() -> String
 extern fn build_system_prompt(ctx: String, chat_mode: Bool) -> String
 extern fn hist_append(hist: String, role: String, content: String) -> String
+extern fn conv_hist_key(session_id: String) -> String
+extern fn conv_hist_label(session_id: String) -> String
+extern fn is_utility_request(body: String, session_id: String) -> Bool
+extern fn provenance_scan_urls(arr: String, acc: String) -> String
+extern fn provenance_add_sources(block: String, btype: String, has_cit: Bool, cit_raw: String, acc: String) -> String
+extern fn provenance_names(tools_used: String) -> String
+extern fn text_join_sep(accumulated: String, incoming: String, after_interruption: Bool) -> String
+extern fn receipt_rule() -> String
+extern fn receipt_strip(s: String) -> String
+extern fn tool_receipt(tools_used: String, sources: String) -> String
 extern fn hist_trim(hist: String) -> String
 extern fn hist_trim_with_bell_guard(hist: String) -> String
 extern fn clean_llm_response(s: String) -> String
-extern fn conv_history_persist(hist: String) -> Void
-extern fn conv_history_load() -> String
+extern fn conv_history_persist(session_id: String, hist: String) -> Void
+extern fn conv_history_load(session_id: String) -> String
+extern fn conv_history_record(session_id: String, user_msg: String, assistant_msg: String, receipt: String) -> Void
+extern fn conv_history_block(session_id: String) -> String
+extern fn layered_generate(prompt: String, imprint_id: String, session_id: String) -> String
 extern fn session_preload_bullets(nodes: String, max_bullets: Int, snip_len: Int) -> String
+extern fn affective_context_prefix() -> String
 extern fn handle_chat(body: String) -> String
 extern fn handle_see(body: String) -> String
 extern fn studio_tools_json() -> String
@@ -37,6 +54,8 @@ extern fn llm_wire_format() -> String
 extern fn json_escape(s: String) -> String
 extern fn openai_chat_complete(model: String, base_url: String, api_key: String, safe_sys: String, messages_json: String) -> String
 extern fn agentic_tools_literal() -> String
+extern fn web_search_tool_json() -> String
+extern fn strip_client_web_search(tools_inner: String) -> String
 extern fn agentic_tools_with_web() -> String
 extern fn connector_tools_json() -> String
 extern fn agentic_tools_all() -> String
@@ -46,6 +65,10 @@ extern fn call_neuron_mcp(tool_name: String, args: String) -> String
 extern fn agent_workspace_root() -> String
 extern fn path_within_root(path: String, root: String) -> Bool
 extern fn resolve_in_root(path: String, root: String) -> String
+extern fn run_command_is_readonly(cmd: String) -> Bool
+extern fn cmd_abs_escape_at(cmd: String, root: String, needle: String) -> Bool
+extern fn run_command_guard(cmd: String, root: String) -> String
+extern fn classify_tool_risk(tool_name: String, tool_input: String) -> String
 extern fn dispatch_tool(tool_name: String, tool_input: String) -> String
 extern fn is_builtin_tool(tool_name: String) -> Bool
 extern fn next_bridge_id() -> String

dist/elp-c-decls.h

@@ -5,6 +5,15 @@ el_val_t add_punct(el_val_t s, el_val_t intent);
 el_val_t add_to_seen(el_val_t seen, el_val_t node_id);
 el_val_t aff_try_slot(el_val_t slot_json, el_val_t aff_7d_ts, el_val_t acc_key);
 el_val_t affective_context_prefix(void);
+el_val_t is_utility_request(el_val_t body, el_val_t session_id);
+el_val_t operator_identity_block(void);
+el_val_t provenance_add_sources(el_val_t block, el_val_t btype, el_val_t has_cit, el_val_t cit_raw, el_val_t acc);
+el_val_t provenance_names(el_val_t tools_used);
+el_val_t provenance_scan_urls(el_val_t arr, el_val_t acc);
+el_val_t text_join_sep(el_val_t accumulated, el_val_t incoming, el_val_t after_interruption);
+el_val_t receipt_rule(void);
+el_val_t receipt_strip(el_val_t s);
+el_val_t tool_receipt(el_val_t tools_used, el_val_t sources);
 el_val_t agent_number(el_val_t agent);
 el_val_t agent_person(el_val_t agent);
 el_val_t agent_workspace_root(void);
@@ -151,8 +160,12 @@ el_val_t cmd_abs_escape_at(el_val_t cmd, el_val_t root, el_val_t needle);
 el_val_t connectd_get(el_val_t suffix);
 el_val_t connectd_post(el_val_t suffix, el_val_t body);
 el_val_t connector_tools_json(void);
-el_val_t conv_history_load(void);
-el_val_t conv_history_persist(el_val_t hist);
+el_val_t conv_hist_key(el_val_t session_id);
+el_val_t conv_hist_label(el_val_t session_id);
+el_val_t conv_history_block(el_val_t session_id);
+el_val_t conv_history_load(el_val_t session_id);
+el_val_t conv_history_persist(el_val_t session_id, el_val_t hist);
+el_val_t conv_history_record(el_val_t session_id, el_val_t user_msg, el_val_t assistant_msg, el_val_t receipt);
 el_val_t cop_article(el_val_t gender, el_val_t number, el_val_t definite);
 el_val_t cop_bwk_future(el_val_t prefix);
 el_val_t cop_bwk_perfect(el_val_t prefix);
@@ -782,7 +795,8 @@ el_val_t lang_profile_uga(void);
 el_val_t lang_profile_zh(void);
 el_val_t lang_profile(el_val_t code, el_val_t word_order, el_val_t morph_type, el_val_t has_case, el_val_t has_gender, el_val_t script_dir, el_val_t agreement, el_val_t null_subject);
 el_val_t lang_word_order(el_val_t profile);
-el_val_t layered_cycle(el_val_t raw_input);
+el_val_t layered_cycle(el_val_t raw_input, el_val_t session_id, el_val_t utility);
+el_val_t layered_generate(el_val_t prompt, el_val_t imprint_id, el_val_t session_id);
 el_val_t lex_class(el_val_t entry);
 el_val_t lex_form(el_val_t entry, el_val_t idx);
 el_val_t lex_pos(el_val_t entry);

dist/neuron-api.c

@@ -10,7 +10,6 @@ el_val_t mem_remember(el_val_t content, el_val_t tags);
 el_val_t mem_recall(el_val_t query, el_val_t depth);
 el_val_t mem_search(el_val_t query, el_val_t limit);
 el_val_t mem_strengthen(el_val_t node_id);
-el_val_t mem_tombstone(el_val_t node_id);
 el_val_t mem_forget(el_val_t node_id);
 el_val_t mem_consolidate(void);
 el_val_t mem_save(el_val_t path);
@@ -361,7 +360,7 @@ el_val_t handle_api_remember(el_val_t body) {
   el_val_t sal = ({ el_val_t _if_result_14 = 0; if (str_eq(sal_str, EL_STR("0.95"))) { _if_result_14 = (el_from_float(0.95)); } else { _if_result_14 = (({ el_val_t _if_result_15 = 0; if (str_eq(sal_str, EL_STR("0.75"))) { _if_result_15 = (el_from_float(0.75)); } else { _if_result_15 = (({ el_val_t _if_result_16 = 0; if (str_eq(sal_str, EL_STR("0.25"))) { _if_result_16 = (el_from_float(0.25)); } else { _if_result_16 = (el_from_float(0.5)); } _if_result_16; })); } _if_result_15; })); } _if_result_14; });
   el_val_t base_tags = ({ el_val_t _if_result_17 = 0; if (str_eq(tags_raw, EL_STR(""))) { _if_result_17 = (EL_STR("[\"Memory\"]")); } else { _if_result_17 = (tags_raw); } _if_result_17; });
   el_val_t final_tags = ({ el_val_t _if_result_18 = 0; if (str_eq(project, EL_STR(""))) { _if_result_18 = (base_tags); } else { el_val_t inner = str_slice(base_tags, 1, (str_len(base_tags) - 1)); _if_result_18 = (el_str_concat(el_str_concat(el_str_concat(el_str_concat(EL_STR("["), inner), EL_STR(",\"project:")), project), EL_STR("\"]"))); } _if_result_18; });
-  el_val_t id = engram_node_full(content, EL_STR("Memory"), EL_STR("memory:remembered"), sal, sal, el_from_float(0.9), EL_STR("Episodic"), final_tags);
+  el_val_t id = engram_node_full(content, EL_STR("Memory"), EL_STR("memory:remembered"), el_from_float(sal), el_from_float(sal), el_from_float(0.9), EL_STR("Episodic"), final_tags);
   if (!api_persisted(id)) {
     return api_not_persisted(id);
   }
@@ -384,7 +383,7 @@ el_val_t handle_api_node_create(el_val_t body) {
   el_val_t tags = ({ el_val_t _if_result_22 = 0; if (str_eq(tags_raw, EL_STR(""))) { _if_result_22 = (el_str_concat(el_str_concat(EL_STR("[\""), node_type), EL_STR("\"]"))); } else { _if_result_22 = (tags_raw); } _if_result_22; });
   el_val_t importance = json_get(body, EL_STR("importance"));
   el_val_t sal = ({ el_val_t _if_result_23 = 0; if (str_eq(importance, EL_STR("critical"))) { _if_result_23 = (el_from_float(0.95)); } else { _if_result_23 = (({ el_val_t _if_result_24 = 0; if (str_eq(importance, EL_STR("high"))) { _if_result_24 = (el_from_float(0.75)); } else { _if_result_24 = (({ el_val_t _if_result_25 = 0; if (str_eq(importance, EL_STR("low"))) { _if_result_25 = (el_from_float(0.25)); } else { _if_result_25 = (el_from_float(0.5)); } _if_result_25; })); } _if_result_24; })); } _if_result_23; });
-  el_val_t id = engram_node_full(content, node_type, label, sal, sal, el_from_float(0.9), tier, tags);
+  el_val_t id = engram_node_full(content, node_type, label, el_from_float(sal), el_from_float(sal), el_from_float(0.9), tier, tags);
   if (!api_persisted(id)) {
     return api_not_persisted(id);
   }
@@ -497,9 +496,8 @@ el_val_t handle_api_capture_knowledge(el_val_t body) {
     return api_err(EL_STR("content is required"));
   }
   el_val_t full = ({ el_val_t _if_result_44 = 0; if (str_eq(title, EL_STR(""))) { _if_result_44 = (content); } else { _if_result_44 = (el_str_concat(el_str_concat(title, EL_STR(": ")), content)); } _if_result_44; });
-  el_val_t lbl = str_slice(title, 0, 80);
   el_val_t tags = EL_STR("[\"Knowledge\",\"captured\"]");
-  el_val_t id = engram_node_full(full, EL_STR("Knowledge"), lbl, el_from_float(0.85), el_from_float(0.8), el_from_float(0.9), EL_STR("Episodic"), tags);
+  el_val_t id = engram_node_full(full, EL_STR("Knowledge"), EL_STR("knowledge:captured"), el_from_float(0.85), el_from_float(0.8), el_from_float(0.9), EL_STR("Episodic"), tags);
   if (!api_persisted(id)) {
     return api_not_persisted(id);
   }
@@ -517,7 +515,7 @@ el_val_t handle_api_evolve_knowledge(el_val_t body) {
     return api_err_protected(prior_id);
   }
   el_val_t tags = EL_STR("[\"Knowledge\",\"evolved\"]");
-  el_val_t new_id = engram_node_full(content, EL_STR("Knowledge"), EL_STR(""), el_from_float(0.75), el_from_float(0.75), el_from_float(0.9), EL_STR("Episodic"), tags);
+  el_val_t new_id = engram_node_full(content, EL_STR("Knowledge"), EL_STR("knowledge:evolved"), el_from_float(0.75), el_from_float(0.75), el_from_float(0.9), EL_STR("Episodic"), tags);
   if (!api_persisted(new_id)) {
     return api_not_persisted(new_id);
   }
@@ -539,7 +537,7 @@ el_val_t handle_api_promote_knowledge(el_val_t body) {
   }
   el_val_t tags_raw = json_get(body, EL_STR("tags"));
   el_val_t tags = ({ el_val_t _if_result_45 = 0; if (str_eq(tags_raw, EL_STR(""))) { _if_result_45 = (EL_STR("[\"Knowledge\",\"tier:canonical\",\"disposition:stable\"]")); } else { _if_result_45 = (tags_raw); } _if_result_45; });
-  el_val_t new_id = engram_node_full(content, EL_STR("Knowledge"), EL_STR(""), el_from_float(0.9), el_from_float(0.9), el_from_float(1.0), EL_STR("Canonical"), tags);
+  el_val_t new_id = engram_node_full(content, EL_STR("Knowledge"), EL_STR("knowledge:canonical"), el_from_float(0.9), el_from_float(0.9), el_from_float(1.0), EL_STR("Canonical"), tags);
   if (!api_persisted(new_id)) {
     return api_not_persisted(new_id);
   }
@@ -710,7 +708,7 @@ el_val_t handle_api_evolve_memory(el_val_t body) {
   el_val_t sal_str = ({ el_val_t _if_result_65 = 0; if (str_eq(importance, EL_STR("critical"))) { _if_result_65 = (EL_STR("0.95")); } else { _if_result_65 = (({ el_val_t _if_result_66 = 0; if (str_eq(importance, EL_STR("high"))) { _if_result_66 = (EL_STR("0.75")); } else { _if_result_66 = (({ el_val_t _if_result_67 = 0; if (str_eq(importance, EL_STR("low"))) { _if_result_67 = (EL_STR("0.25")); } else { _if_result_67 = (EL_STR("0.50")); } _if_result_67; })); } _if_result_66; })); } _if_result_65; });
   el_val_t sal = ({ el_val_t _if_result_68 = 0; if (str_eq(sal_str, EL_STR("0.95"))) { _if_result_68 = (el_from_float(0.95)); } else { _if_result_68 = (({ el_val_t _if_result_69 = 0; if (str_eq(sal_str, EL_STR("0.75"))) { _if_result_69 = (el_from_float(0.75)); } else { _if_result_69 = (({ el_val_t _if_result_70 = 0; if (str_eq(sal_str, EL_STR("0.25"))) { _if_result_70 = (el_from_float(0.25)); } else { _if_result_70 = (el_from_float(0.5)); } _if_result_70; })); } _if_result_69; })); } _if_result_68; });
   el_val_t tags = EL_STR("[\"Memory\",\"evolved\"]");
-  el_val_t new_id = engram_node_full(content, EL_STR("Memory"), EL_STR("memory:evolved"), sal, sal, el_from_float(0.9), EL_STR("Episodic"), tags);
+  el_val_t new_id = engram_node_full(content, EL_STR("Memory"), EL_STR("memory:evolved"), el_from_float(sal), el_from_float(sal), el_from_float(0.9), EL_STR("Episodic"), tags);
   if (!str_eq(prior_id, EL_STR("")) && !str_eq(new_id, EL_STR(""))) {
     engram_connect(new_id, prior_id, el_from_float(0.9), EL_STR("supersedes"));
   }
@@ -785,7 +783,7 @@ el_val_t handle_api_cultivate(el_val_t body) {
     el_val_t importance = json_get(body, EL_STR("importance"));
     el_val_t sal = ({ el_val_t _if_result_71 = 0; if (str_eq(importance, EL_STR("critical"))) { _if_result_71 = (el_from_float(0.95)); } else { _if_result_71 = (({ el_val_t _if_result_72 = 0; if (str_eq(importance, EL_STR("high"))) { _if_result_72 = (el_from_float(0.75)); } else { _if_result_72 = (({ el_val_t _if_result_73 = 0; if (str_eq(importance, EL_STR("low"))) { _if_result_73 = (el_from_float(0.25)); } else { _if_result_73 = (el_from_float(0.5)); } _if_result_73; })); } _if_result_72; })); } _if_result_71; });
     el_val_t tags = EL_STR("[\"Memory\",\"evolved\",\"cultivated\"]");
-    el_val_t new_id = engram_node_full(content, EL_STR("Memory"), EL_STR("memory:cultivated"), sal, sal, el_from_float(0.9), EL_STR("Episodic"), tags);
+    el_val_t new_id = engram_node_full(content, EL_STR("Memory"), EL_STR("memory:cultivated"), el_from_float(sal), el_from_float(sal), el_from_float(0.9), EL_STR("Episodic"), tags);
     if (!str_eq(prior_id, EL_STR("")) && !str_eq(new_id, EL_STR(""))) {
       engram_connect(new_id, prior_id, el_from_float(0.9), EL_STR("supersedes"));
     }
@@ -828,8 +826,8 @@ el_val_t handle_api_consolidate(el_val_t body) {
   el_val_t summary = json_get(body, EL_STR("summary"));
   el_val_t snap = state_get(EL_STR("soul_snapshot_path"));
   if (!str_eq(snap, EL_STR(""))) {
-    el_val_t saved = engram_save(snap);
-    if (saved == 0) {
+    el_val_t save_result = engram_save(snap);
+    if (str_eq(save_result, EL_STR(""))) {
       println(el_str_concat(el_str_concat(EL_STR("[api] consolidate: engram_save failed for "), snap), EL_STR(" \xe2\x80\x94 snapshot may be out of sync")));
     }
   }

dist/neuron.c

@@ -541,7 +541,7 @@ int main(int _argc, char** _argv) {
   axon_raw = env(EL_STR("NEURON_API_URL"));
   axon_base = ({ el_val_t _if_result_47 = 0; if (str_eq(axon_raw, EL_STR(""))) { _if_result_47 = (EL_STR("http://localhost:7771")); } else { _if_result_47 = (axon_raw); } _if_result_47; });
   studio_dir_raw = env(EL_STR("SOUL_STUDIO_DIR"));
-  studio_dir = ({ el_val_t _if_result_48 = 0; if (str_eq(studio_dir_raw, EL_STR(""))) { _if_result_48 = (EL_STR("/Users/will/Development/neuron-technologies/products/cgi-studio/el-daemon")); } else { _if_result_48 = (studio_dir_raw); } _if_result_48; });
+  studio_dir = ({ el_val_t _if_result_48 = 0; if (str_eq(studio_dir_raw, EL_STR(""))) { _if_result_48 = (el_str_concat(env(EL_STR("HOME")), EL_STR("/Development/neuron-technologies/products/cgi-studio/el-daemon"))); } else { _if_result_48 = (studio_dir_raw); } _if_result_48; });
   println(el_str_concat(el_str_concat(el_str_concat(EL_STR("[soul] boot - cgi="), soul_cgi_id), EL_STR(" port=")), int_to_str(port)));
   using_http_engram = !str_eq(engram_url_raw, EL_STR(""));
   engram_load(snapshot);

dist/soul-with-nlg.el

@@ -1,3 +1,18 @@
+// ╔══════════════════════════════════════════════════════════════════════════╗
+// ║ STALE BUNDLE — DO NOT BUILD. UNSAFE CHAT PATH.                           ║
+// ╚══════════════════════════════════════════════════════════════════════════╝
+// This concatenated bundle is a snapshot, not a source of truth, and it is stale in
+// a way that matters for safety: it wires /api/chat straight to handle_chat and
+// contains NO layered_cycle at all (verified: zero occurrences in the bundled code —
+// the only textual hit in this file is this banner). A binary built from
+// this file would run chat with no enforcing input gate (no safety_screen, no
+// hard-bell short-circuit) and no enforcing output gate (no safety_validate).
+//
+// Build from the .el sources via manifest.el (entry soul.el), or from dist/soul.c.
+// Nothing in the repo references this file. It is kept only as a historical artifact
+// and should be deleted once Will confirms nothing external depends on it.
+// (Flagged 2026-08-04 in _engine-websearch-20260804/SAFETY-STOP.md; banner added
+// 2026-08-05 with the plain-chat generation fix.)
 // language-profile.el - Language profile data and accessors.
 //
 // A language profile is a slot map ([String] key-value list) describing the
@@ -21304,7 +21319,7 @@ println("[memory] consolidate stats=" + stats)
 let soul_axon_base_raw: String = env("NEURON_API_URL")
 let soul_axon_base: String = if str_eq(soul_axon_base_raw, "") { "http://localhost:7771" } else { soul_axon_base_raw }
 let soul_token: String = env("NEURON_TOKEN")
-let soul_studio_ui_dir: String = "/Users/will/Development/neuron-technologies/products/cgi-studio/el-daemon"
+let soul_studio_ui_dir: String = env("HOME") + "/Development/neuron-technologies/products/cgi-studio/el-daemon"
 
 // ── Runtime bridge helpers ────────────────────────────────────────────────────
 

dist/soul.c.stamp

@@ -0,0 +1,18 @@
+# soul.c.stamp — fingerprint of the .el sources dist/soul.c was generated from.
+# Written by tools/soulc-stamp.sh --write. Do not hand-edit.
+# generated_amalgam_sha256 ee09798ad93ddd047136577cf324483e5956984d60d06596d34662f315ee0df4
+# generated_amalgam_bytes  1204845
+f8597e10546654bce3fbbe40461b2da59d0e06dbf1b038d1d362d24f949e3911  awareness.el
+b6f3d14ca0c26017a2d617399a6d3754dabb0905e4d5f52eb75d25c4ad18d3c5  chat.el
+42288c212cbf72fb1e8ecbd4d9900e4e9ee1cfa475b7974295c7637f1bf2939f  elp-input.el
+b3f77f49d6086932c38bd17fe7a5eaf8bce25685f6fc3e1750f05729c6b49b9e  imprint.el
+fba8ffdb9ba72bca5b09ca1c93a520edc52f3f4d8aec2c7585fe9b17e06420b2  manifest.el
+550a72e234ae8cec1f33e02108fd365353f45edd88513da90b792e79b6c0e5f0  memory.el
+5ec07ec9785b02abe32f3ff7acf2d1f9f7e07c0967fac97e6eff17d7110b5c84  neuron-api.el
+03c47c451e0e87f2c252cadb4b765867943962a804f548dd53adeef0520912c8  persist.el
+a6d69f3fc55233d9d3300160fd46a1551f2064bcd0fb84e2c9e432f636a72476  routes.el
+c28e36952ec56525963a0bdf29455ab097d3b0c5653d19c25fbb005e1069a1f7  safety.el
+fd3ab91d0ae0ea26639e21bef2f8f94054dc4b02eae68b19e3fe689d2769aad4  sessions.el
+5613b60d74d5d7768f46da5ac435a5dd99d38c27f0f7013c89fa27e98dc8a21c  soul.el
+30337940905171a9645b0929f0a412ce6b3dccb1246495070c553bca0bbae6cd  stewardship.el
+e105dc5990e6adbf39db9dc0462cd8bcf6e6c3dfd03709059227ecfad2bbab29  studio.el

docs/NARRATED-RUNS-ENGINE-NOTES-20260713.md

@@ -0,0 +1,34 @@
+# Narrated runs — engine notes for Will (2026-07-13)
+
+Source half: commit aa67f86 on feat/agent-phase1-soul (run-progress ledger,
+`/api/run-progress/<sid>` route, narration on the pause envelope, config display
+default). E2E-verified via the compiled test bed on Tim's clean profile.
+
+Compiled-form-only fixes (in `neuron-container-build/soul-narrated-runs-20260713.patch`,
+applies ON TOP of `soul-webfix-20260711.patch` — these need porting to chat.el when the
+webfix itself is ported):
+
+1. **pause_turn + tool_use interleave**: a pause_turn response can ALSO carry a client
+   tool_use; resuming verbatim leaves it unpaired → Anthropic 400 "tool_use ids were
+   found without tool_result". Fix: tool-bearing pause rounds are tool turns
+   (dispatch + pair); verbatim resume only when the round has no client tool.
+2. **Agentic toolset scope**: agentic_tools_all() fed EVERY connector/MCP tool (Notion,
+   code-execution…) into the loop. Code-execution flips the API into programmatic
+   tool calling, whose pairing protocol the single-tool manual loop does not speak —
+   source of the dangling-pair 400s AND the bash_code_execution workspace-dodge.
+   Fix: handle_chat_agentic declares builtins + ONE server web_search only.
+   Connector tools return when the loop gains real multi-tool/programmatic support.
+3. **disable_parallel_tool_use: true** on agentic requests — the loop captures only the
+   first tool_use per round; Opus-class models parallel-call. Enforce the invariant.
+4. **web_search server-tool default variant → web_search_20250305 (GA)**. The 20260209
+   variant couples to code-execution ⇒ programmatic mode (see #2, and the June note:
+   "inert unless code-execution attached").
+5. **Homegrown web_search removed** from the tool catalog (server-side is the one tool).
+
+Known engine debts this work surfaced (not fixed):
+
+- **Poisoned session history**: a failed run persists the malformed assistant turn; every
+  later turn in that session replays it and 400s. Needs history sanitation on load.
+- **Huge-history invalid-escape 400** (~346KB request) — likely the same poisoned blob.
+- **macOS note**: replacing a binary in place invalidates its ad-hoc signature (instant
+  silent SIGKILL, looks like exit 0). `rm + cp + codesign -f -s -` is the swap ritual.

mcp-wrapper/src/main.el

@@ -110,7 +110,7 @@ tool("beginSession", "Initialize session: surface recent high-importance memorie
 "," + tool("linkCausal", "Create a causal edge (cause -> effect).") +
 "," + tool("restructureCausalGraph", "Re-balance the causal subgraph after new evidence.") +
 "," + tool("rebuildGraph", "Rebuild graph indices from the on-disk snapshot.") +
-"," + tool("runStructuralAudit", "Audit graph structure for orphans, dangling edges, mislabeled types.") +
+"," + tool("runStructuralAudit", "Stage 1 structural audit: owner-vs-runtime divergence, orphans and dangling edges, typed-edge distribution, self-model connectivity. Returns an annotated characterization, not a score.") +
 // ── Backlog + work ──────────────────────────────────────────────────────────
 "," + tool("planWork", "Create a backlog item.") +
 "," + tool("reviewBacklog", "Browse work items.") +
@@ -311,8 +311,25 @@ fn delete_by_id(args: String) -> String {
     if str_eq(id, "") {
         return mcp_text_result("error: id is required")
     }
-    // Soul does not yet expose a delete HTTP route; acknowledge the request
-    return mcp_json_result("{\"ok\":true,\"deleted\":\"" + id + "\",\"note\":\"soft-deleted\"}")
+    // BUG-18 (Receipt Contract rule 1): this handler used to FABRICATE
+    // {"ok":true,...,"note":"soft-deleted"} without calling the soul at all —
+    // a false receipt for every delete-family tool (removeKnowledge,
+    // deleteProcess, deleteImprint, dischargeWonder). The old "soul does not
+    // yet expose a delete HTTP route" note was stale: /api/neuron/node/delete
+    // tombstones any node type and errors on unknown ids. Route there and
+    // propagate the soul's real answer.
+    let body: String = "{\"id\":\"" + id + "\"}"
+    let resp: String = http_post_json(neuron_url() + "/node/delete", body)
+    if !str_contains(resp, "\"ok\":true") {
+        return mcp_json_result(resp)
+    }
+    // Read-back verify before answering ok: the tombstone marker
+    // (label "tombstone:<id>") must actually be wired to the node.
+    let check: String = http_get(neuron_url() + "/graph?id=" + id + "&depth=1")
+    if !str_contains(check, "tombstone:" + id) {
+        return mcp_json_result("{\"ok\":false,\"error\":\"delete_not_persisted\",\"id\":\"" + id + "\"}")
+    }
+    return mcp_json_result(resp)
 }
 
 // evolve_by_supersede: create an updated node and wire a supersedes edge.
@@ -546,6 +563,18 @@ fn tool_forget(args: String) -> String {
     // Previously this returned a fake ok without deleting OR tombstoning anything.
     let body: String = "{\"id\":\"" + id + "\"}"
     let resp: String = http_post_json(neuron_url() + "/memory/delete", body)
+    // BUG-18 (Receipt Contract rule 1): propagate the soul's real answer — its
+    // errors (memory not found, protected node, transport failure) pass through
+    // unchanged — and never answer ok without read-back.
+    if !str_contains(resp, "\"ok\":true") {
+        return mcp_json_result(resp)
+    }
+    // Read-back verify before answering ok: the tombstone marker
+    // (label "tombstone:<id>") must actually be wired to the node.
+    let check: String = http_get(neuron_url() + "/graph?id=" + id + "&depth=1")
+    if !str_contains(check, "tombstone:" + id) {
+        return mcp_json_result("{\"ok\":false,\"error\":\"delete_not_persisted\",\"id\":\"" + id + "\"}")
+    }
     return mcp_json_result(resp)
 }
 
@@ -651,7 +680,16 @@ fn dispatch_tool_call(tool_name: String, args: String) -> String {
         return mcp_json_result(resp)
     }
     if str_eq(tool_name, "runStructuralAudit") {
-        let resp: String = http_get(neuron_url() + "/session/begin")
+        // Was: GET /session/begin — an unrelated session digest returned under an
+        // audit tool name, i.e. the tool advertised a check that did not exist.
+        // Now points at the real Stage 1 route (neuron-api.el
+        // handle_api_structural_audit). Sample caps ride the query string; the
+        // defaults keep a manual audit to a couple of seconds.
+        let e_s: Int = json_get_int(args, "edge_sample")
+        let n_s: Int = json_get_int(args, "node_sample")
+        let qs: String = "?edge_sample=" + int_to_str(if e_s > 0 { e_s } else { 3000 })
+            + "&node_sample=" + int_to_str(if n_s > 0 { n_s } else { 300 })
+        let resp: String = http_get(neuron_url() + "/audit/structural" + qs)
         return mcp_json_result(resp)
     }
 

memory.el

@@ -1,9 +1,91 @@
+import "persist.el"
+
 fn tier_working() -> String { return "Working" }
 fn tier_episodic() -> String { return "Episodic" }
 fn tier_canonical() -> String { return "Canonical" }
 
+// ── Association on write ──────────────────────────────────────────────────────
+// DESIGN: "promotion integrates candidate nodes by linking them to existing nodes
+// using typed semantic edges RATHER THAN APPENDING AS UNLINKED CONTENT" (CCR
+// claim 29). Unlinked append is the explicitly rejected behaviour — and it is the
+// only behaviour this system had. Measured 2026-08-09 on Tim's graph: 14,214 edges
+// across 80,936 nodes, 5% of nodes connected to anything, and NO edge created by
+// any write since 2026-07-19 while 27,000+ nodes were added. A memory that forms
+// no connections cannot be reached by spreading activation, so retrieval silently
+// degrades to literal matching.
+//
+// BOUNDS, each one bought with a specific failure:
+//   * max 3 edges per memory — link_memories.py's cap, precision over spray
+//   * never link to identity (self/*, Value): the existing policy is explicit that
+//     "memories must not pollute the self traversal by similarity; only an explicit
+//     citation may touch identity". Similarity is not citation.
+//   * never link telemetry (state-event, soul-response, boot_count, loop-outcome):
+//     these are ~97% of daily write volume (1,020 vs 31 real memories on 08-08).
+//     Linking them would add ~3,000 noise edges a day and re-flatten the graph in
+//     the name of connecting it.
+//   * fail-soft: a failed association never fails the write.
+// Edges go through wt_edge so they reach the owner and survive restart.
+fn mem_assoc_skip_label(label: String) -> Bool {
+    if str_contains(label, "state-event")   { return true }
+    if str_contains(label, "soul-response") { return true }
+    if str_contains(label, "soul-outbox")   { return true }
+    if str_contains(label, "boot_count")    { return true }
+    if str_contains(label, "loop-outcome")  { return true }
+    if str_contains(label, "search-result") { return true }
+    return false
+}
+
+// A candidate is linkable only if it is a real, distinct, non-identity node.
+fn mem_assoc_ok(cand_id: String, cand_label: String, self_id: String) -> Bool {
+    if str_eq(cand_id, "") { return false }
+    if str_eq(cand_id, self_id) { return false }
+    // CASE MATTERS — measured 2026-08-09. A lowercase-only check let a memory link
+    // to "Self — Values (grounded)", i.e. it polluted the self traversal, which is
+    // the one thing this policy exists to prevent. My verification had the same
+    // blind spot and printed PASS. Check every casing the graph actually uses, and
+    // exclude identity node TYPES as well as labels.
+    let lab: String = str_lower(cand_label)
+    if str_starts_with(lab, "self") { return false }
+    if str_starts_with(lab, "value") { return false }
+    if str_contains(lab, "values") { return false }
+    if str_contains(lab, "identity") { return false }
+    if mem_assoc_skip_label(cand_label) { return false }
+    return true
+}
+
+// One slot of the association. Manual unroll rather than a loop: EL's codegen
+// mis-emits accumulating while-loops (documented at soul.el:212, which unrolled
+// three affective slots for the same reason).
+fn mem_assoc_slot(results: String, idx: Int, new_id: String) -> Void {
+    if idx >= json_array_len(results) { return }
+    let cand: String = json_array_get(results, idx)
+    let cid: String = json_get(cand, "id")
+    let clabel: String = json_get(cand, "label")
+    let ctype: String = json_get(cand, "node_type")
+    if str_eq(ctype, "Value") { return }
+    if str_eq(ctype, "DharmaSelf") { return }
+    if str_eq(ctype, "Safety") { return }
+    if mem_assoc_ok(cid, clabel, new_id) {
+        wt_edge(new_id, cid, el_from_float(0.5), "related")
+    }
+}
+
+// mem_associate — connect a freshly written memory to what it is about.
+fn mem_associate(new_id: String, content: String, label: String) -> Void {
+    if str_eq(new_id, "") { return }
+    if mem_assoc_skip_label(label) { return }
+    // Ask the graph what this memory resembles. Now that the store carries
+    // meaning-vectors this is semantic, not merely lexical.
+    let probe: String = str_slice(content, 0, 400)
+    let results: String = engram_recall_json(probe, 4)
+    if str_eq(results, "") { return }
+    mem_assoc_slot(results, 0, new_id)
+    mem_assoc_slot(results, 1, new_id)
+    mem_assoc_slot(results, 2, new_id)
+}
+
 fn mem_store(content: String, label: String, tags: String) -> String {
-    let id: String = engram_node_full(
+    let id: String = wt_node(
         content,
         "Memory",
         label,
@@ -17,13 +99,26 @@ fn mem_store(content: String, label: String, tags: String) -> String {
         println("[memory] write rejected by engram (empty id): label=" + label)
         return ""
     }
-    // Read back to verify the node actually persisted — guards against silent write failures.
-    let readback: String = engram_get_node_json(id)
-    if str_eq(readback, "") || str_eq(readback, "{}") {
-        println("[memory] WRITE VERIFY FAILED: label=" + label + " id=" + id + " — node absent after write")
-        return ""
+    // wt_node has already read the node back locally and returns "" if it did
+    // not land, so the old duplicate read-back here is gone.
+    //
+    // HONESTY (neuron#117): the receipt now says WHERE the write is.
+    // The old unconditional "write verified" line asserted against the soul's
+    // own RAM — true in memory, false on disk — and printed ~115,000 times on
+    // Tim's machine while the canonical snapshot sat frozen for three days.
+    // wt_commit flushes the spool and then asks the OWNER. When it says false
+    // the node is real and recallable but not yet durable, and the log says so
+    // rather than claiming a save that did not happen. The id is still returned:
+    // the local write DID succeed, and the queued delta will be retried.
+    let durable: Bool = wt_commit(id)
+    // Associate AFTER the node is durable: an edge to a node that did not persist
+    // is a dangling edge, which is the defect the 2026-08-09 cleanup removed 830 of.
+    mem_associate(id, content, label)
+    if durable {
+        println("[memory] write persisted at owner: " + id + " label=" + label)
+    } else {
+        println("[memory] write IN MEMORY ONLY (queued for owner, not yet durable): " + id + " label=" + label)
     }
-    println("[memory] write verified: " + id + " ok")
     return id
 }
 
@@ -51,12 +146,12 @@ fn mem_strengthen(node_id: String) -> Void {
 // memory.el (imported first) so awareness.el and neuron-api.el can both call it.
 fn mem_tombstone(node_id: String) -> String {
     let tags: String = "[\"Tombstone\",\"status:deleted\"]"
-    let marker: String = engram_node_full(
+    let marker: String = wt_node(
         node_id, "Tombstone", "tombstone:" + node_id,
         el_from_float(0.01), el_from_float(0.01), el_from_float(1.0),
         "Episodic", tags)
     if !str_eq(marker, "") {
-        engram_connect(marker, node_id, el_from_float(1.0), "tombstones")
+        wt_edge(marker, node_id, el_from_float(1.0), "tombstones")
     }
     return marker
 }

neuron-api.el

@@ -59,8 +59,14 @@ fn api_query_param(path: String, key: String) -> String {
     if pos < 0 { return "" }
     let after: String = str_slice(qs, pos + str_len(needle), str_len(qs))
     let amp: Int = str_index_of(after, "&")
-    if amp < 0 { return after }
-    return str_slice(after, 0, amp)
+    let raw: String = if amp < 0 { after } else { str_slice(after, 0, amp) }
+    // URL-decode the extracted value BEFORE any downstream tokenizing. Clients
+    // percent-encode spaces (%20) and form-encode them as '+', so a multi-word
+    // query like "foo bar" arrives as "foo%20bar" / "foo+bar". Left undecoded,
+    // the ranked lexical search sees a single un-splittable token and matches
+    // nothing (single-word queries still hit). url_decode maps '+' -> space
+    // and %XX -> byte, restoring the word boundaries for recall + knowledge search.
+    return url_decode(raw)
 }
 
 fn api_query_int(path: String, key: String, default_val: Int) -> Int {
@@ -189,15 +195,24 @@ fn api_compact_activated(raw: String, max_items: Int, snip: Int) -> String {
 }
 
 // api_persisted — read-back-after-write guard against hallucinated saves.
-// After a write builtin returns an id, confirm the node is actually queryable
-// via engram_get_node_json(id) (returns "" or "null" when missing). Returns
-// true only when the node is genuinely persisted.
+//
+// WIDENED FOR neuron#117. This function is the single gate every MCP write
+// handler passes through before it reports success (10 call sites), which makes
+// it the right place to close the honesty gap rather than editing ten receipts.
+//
+// It used to read back from engram_get_node_json — the SOUL'S OWN in-process
+// graph. In HTTP-engram mode that asserts the wrong thing: the soul is not the
+// persistence owner, so a node present in its RAM and absent from the owner read
+// as "persisted" and then vanished on the next restart. The guard was doing
+// exactly what its comment promised and still certifying writes that did not
+// survive. It now flushes the write-through spool and asks the OWNER.
+//
+// In file mode (no ENGRAM_URL) the soul IS the owner and wt_commit collapses to
+// the original local read-back — unchanged behaviour, which is what keeps this
+// reversible.
 fn api_persisted(id: String) -> Bool {
     if str_eq(id, "") { return false }
-    let node: String = engram_get_node_json(id)
-    // engram_get_node_json returns "{}" (empty object) when node is not found — not "" or "null".
-    // Check all three to guard against any runtime variation.
-    return !str_eq(node, "") && !str_eq(node, "null") && !str_eq(node, "{}")
+    return wt_commit(id)
 }
 
 // api_not_persisted — standard error for a write that did not read back.
@@ -271,32 +286,53 @@ fn memory_hide_tombstoned(raw: String, path: String) -> String {
 // Spread-activates from session intent, loads self-root neighbors,
 // surfaces recent InternalStateEvent nodes, returns stats + recent nodes.
 fn handle_api_begin_session(body: String) -> String {
-    // PAYLOAD BOUND (2026-07-30 self-review): this handler was the only
-    // working-set endpoint that concatenated UNBOUNDED engram queries —
+    // PAYLOAD BOUND: this handler was the highest-fanout working-set endpoint —
     // a depth-2 spread PLUS the full neighbor dump of the self-identity hub
-    // (highest-fanout node in the graph, ~80KB alone; node JSON carries full
-    // content + embeddings). On the ~12k-node store the assembled response
-    // ran to multiple MB, then roughly doubled through two rounds of JSON
-    // re-escaping in the MCP wrapper — the client saw "socket connection
-    // closed unexpectedly" on every beginSession call. Fix: depth-2 → depth-1
-    // spread, and drop the self-hub dump entirely (identity loading has its
-    // own dedicated tool, inspectGraph; duplicating it here served nothing).
-    // self_neighbors key retained as [] for response-shape compatibility.
+    // (~90KB alone; node JSON carries full content + embeddings). On the ~12k-node
+    // store the assembled response ran to ~900KB, then roughly doubled through two
+    // rounds of JSON re-escaping in the MCP wrapper — the client saw "socket
+    // connection closed unexpectedly" on every beginSession call. Fix: depth-2 →
+    // depth-1 spread, drop the self-hub dump (identity loading has its own tool,
+    // inspectGraph), cap every list, and project each node to a light identity +
+    // a bounded, UTF-8-safe content snippet. self_neighbors kept as [] for
+    // response-shape compatibility. Response drops ~900KB → ~12KB; full content
+    // stays available on demand via recall / fetch / inspectGraph.
     let stats: String = engram_stats_json()
-    // PAYLOAD BOUND (2026-07-31): compact every list to a digest. The raw
-    // activate/scan builtins emit FULL node objects (content up to ~90KB each);
-    // unbounded concatenation reached ~900KB and closed the MCP client socket.
-    // Cap counts + project to identity + UTF-8-safe content snippets → <~150KB.
     let activated_raw: String = engram_activate_json("session start recent memory important", 1)
     let activated: String = api_compact_activated(activated_raw, 8, 240)
     let state_events_raw: String = engram_scan_nodes_by_type_json("InternalStateEvent", 5, 0)
     let state_events: String = api_compact_node_array(state_events_raw, 5, 500)
     let recent_raw: String = engram_scan_nodes_json(10, 0)
     let recent: String = api_compact_node_array(recent_raw, 10, 240)
+    // SELF-SEEDED SLICE (2026-08-09). The design is explicit: "Every compilation
+    // query begins at the self-model node and traverses outward... structural
+    // reachability from the self-model node is a precondition for any node to
+    // appear in compiled context" (will-anderson patents/drafts/engram-claims.md,
+    // Self-Seeded Activation; DRAFT, not a filed provisional — cite it as such).
+    //
+    // Measured 2026-08-09 before this change: compiled context contained 0-1
+    // identity records out of 10, because compilation seeds from a hardcoded
+    // TEXT STRING, never from the self. Even an explicit "my values identity who
+    // I am" query returned a boot counter and state-events.
+    //
+    // This restores the designed behaviour WITHOUT repeating the failure that got
+    // self_neighbors set to [] in the first place: that was an UNBOUNDED ~90KB
+    // neighbour dump which closed the socket on every call. Same bound as every
+    // other list here — cap 8, 240-char snippets. The self root has 34 direct
+    // neighbours of which 23 are identity records, so depth 1 is dense enough to
+    // be worth seeding and small enough to stay cheap.
+    let self_raw: String = engram_neighbors_json("kn-efeb4a5b-5aff-4759-8a97-7233099be6ee", 1, "both")
+    // Cap 24, not 8: measured 2026-08-09, the self root's first 8 neighbours are
+    // TAG nodes ("neuron", "tier:note", "disposition:experimental", "imprint",
+    // "traversal") which crowd out the substantive identity records behind them.
+    // The root has 34 neighbours of which 23 are identity; 24 captures them while
+    // staying bounded. Cost measured at ~+4KB on a ~12KB response, nowhere near
+    // the ~90KB unbounded dump that closed sockets and got this set to [].
+    let self_slice: String = api_compact_node_array(self_raw, 24, 240)
     return "{\"stats\":" + stats
         + ",\"recent\":" + recent
         + ",\"activated\":" + activated
-        + ",\"self_neighbors\":[]"
+        + ",\"self_neighbors\":" + self_slice
         + ",\"recent_state_events\":" + state_events + "}"
 }
 
@@ -304,9 +340,9 @@ fn handle_api_begin_session(body: String) -> String {
 // Spread-activates from "active work" intent + recent nodes.
 fn handle_api_compile_ctx(body: String) -> String {
     let stats: String = engram_stats_json()
-    // PAYLOAD BOUND (2026-07-31): same digest treatment as begin_session. This
-    // handler's depth-2 spread returns even more full nodes, so bounding here is
-    // essential — cap to 10 activated + 20 recent, project to snippets.
+    // PAYLOAD BOUND: same digest treatment as begin_session. This handler's
+    // depth-2 spread returns even more full nodes, so bounding here is essential —
+    // cap to 10 activated + 20 recent, project to UTF-8-safe snippets.
     let activated_raw: String = engram_activate_json("active work context current task in progress", 2)
     let activated: String = api_compact_activated(activated_raw, 10, 240)
     let recent_raw: String = engram_scan_nodes_json(20, 0)
@@ -340,10 +376,17 @@ fn handle_api_remember(body: String) -> String {
         let inner: String = str_slice(base_tags, 1, str_len(base_tags) - 1)
         "[" + inner + ",\"project:" + project + "\"]"
     }
-    let id: String = engram_node_full(content, "Memory", "memory:remembered",
+    let id: String = wt_node(content, "Memory", "memory:remembered",
         sal, sal, el_from_float(0.9),
         "Episodic", final_tags)
     if !api_persisted(id) { return api_not_persisted(id) }
+    // Associate on write (2026-08-09). THIS CALL MUST BE HERE, not only in mem_store.
+    // The HTTP memory route writes via wt_node directly; mem_store serves only the
+    // awareness paths (soul-response, search-result, activation-result) which are
+    // exactly the telemetry we refuse to link. Hooking mem_store alone produced
+    // ZERO edges across four real writes — measured, not assumed, which is the only
+    // reason it was caught before shipping.
+    mem_associate(id, content, "memory:remembered")
     return "{\"id\":\"" + id + "\",\"ok\":true}"
 }
 
@@ -367,7 +410,7 @@ fn handle_api_node_create(body: String) -> String {
             if str_eq(importance, "low") { 0.25 } else { 0.5 }
         }
     }
-    let id: String = engram_node_full(content, node_type, label,
+    let id: String = wt_node(content, node_type, label,
         sal, sal, el_from_float(0.9),
         tier, tags)
     if !api_persisted(id) { return api_not_persisted(id) }
@@ -420,11 +463,11 @@ fn handle_api_node_update(body: String) -> String {
     }
     let body_tags: String = json_get(body, "tags")
     let tags: String = if str_eq(body_tags, "") { "[\"" + node_type + "\"]" } else { body_tags }
-    let new_id: String = engram_node_full(content, node_type, label,
+    let new_id: String = wt_node(content, node_type, label,
         el_from_float(0.5), el_from_float(0.5), el_from_float(0.8),
         tier, tags)
     if !api_persisted(new_id) { return api_not_persisted(new_id) }
-    engram_connect(new_id, id, el_from_float(0.9), "supersedes")
+    wt_edge(new_id, id, el_from_float(0.9), "supersedes")
     return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + id + "\",\"ok\":true}"
 }
 
@@ -448,7 +491,12 @@ fn handle_api_recall(method: String, path: String, body: String) -> String {
     if str_eq(eff_q, "") {
         return api_or_empty(engram_scan_nodes_json(limit, 0))
     }
-    let results: String = engram_search_json(eff_q, limit)
+    // engram_recall_json, not engram_search_json: this route IS the retrieval
+    // surface (claim 24's "embedding search queries"), so it gets the semantic
+    // and associative legs. engram_search_json stays lexical because ~40
+    // internal call sites pass a KEY and seven of them delete every record
+    // that comes back — see the boundary note above eg_search_json_impl.
+    let results: String = engram_recall_json(eff_q, limit)
     return api_or_empty(results)
 }
 
@@ -496,7 +544,7 @@ fn handle_api_capture_knowledge(body: String) -> String {
     let full: String = if str_eq(title, "") { content } else { title + ": " + content }
     let lbl: String = str_slice(title, 0, 80)
     let tags: String = "[\"Knowledge\",\"captured\"]"
-    let id: String = engram_node_full(full, "Knowledge", lbl,
+    let id: String = wt_node(full, "Knowledge", lbl,
         el_from_float(0.85), el_from_float(0.8), el_from_float(0.9),
         "Episodic", tags)
     if !api_persisted(id) { return api_not_persisted(id) }
@@ -511,12 +559,12 @@ fn handle_api_evolve_knowledge(body: String) -> String {
     if !str_eq(prior_id, "") && is_protected_node(prior_id) { return api_err_protected(prior_id) }
     let tags: String = "[\"Knowledge\",\"evolved\"]"
     // Empty label → engram_node_full derives content[:60] (LABEL FIX 2026-07-23).
-    let new_id: String = engram_node_full(content, "Knowledge", "",
+    let new_id: String = wt_node(content, "Knowledge", "",
         el_from_float(0.75), el_from_float(0.75), el_from_float(0.9),
         "Episodic", tags)
     if !api_persisted(new_id) { return api_not_persisted(new_id) }
     if !str_eq(prior_id, "") {
-        engram_connect(new_id, prior_id, el_from_float(0.9), "supersedes")
+        wt_edge(new_id, prior_id, el_from_float(0.9), "supersedes")
     }
     return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\",\"ok\":true}"
 }
@@ -533,11 +581,11 @@ fn handle_api_promote_knowledge(body: String) -> String {
         "[\"Knowledge\",\"tier:canonical\",\"disposition:stable\"]"
     } else { tags_raw }
     // Empty label → engram_node_full derives content[:60] (LABEL FIX 2026-07-23).
-    let new_id: String = engram_node_full(content, "Knowledge", "",
+    let new_id: String = wt_node(content, "Knowledge", "",
         el_from_float(0.9), el_from_float(0.9), el_from_float(1.0),
         "Canonical", tags)
     if !api_persisted(new_id) { return api_not_persisted(new_id) }
-    engram_connect(new_id, prior_id, el_from_float(0.95), "supersedes")
+    wt_edge(new_id, prior_id, el_from_float(0.95), "supersedes")
     return "{\"ok\":true,\"new_id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\"}"
 }
 
@@ -560,7 +608,7 @@ fn handle_api_define_process(body: String) -> String {
     if str_eq(content, "") { return api_err("content is required") }
     let label: String = if str_eq(name, "") { "process:unnamed" } else { "process:" + name }
     let tags: String = "[\"Process\"]"
-    let id: String = engram_node_full(content, "Process", label,
+    let id: String = wt_node(content, "Process", label,
         el_from_float(0.8), el_from_float(0.8), el_from_float(0.9),
         "Canonical", tags)
     if !api_persisted(id) { return api_not_persisted(id) }
@@ -645,7 +693,7 @@ fn handle_api_tune_config(body: String) -> String {
     if str_eq(key, "") { return api_err("key is required") }
     let content: String = "config:" + key + "=" + value
     let tags: String = "[\"ConfigEntry\",\"config\"]"
-    let id: String = engram_node_full(content, "ConfigEntry", key,
+    let id: String = wt_node(content, "ConfigEntry", key,
         el_from_float(0.85), el_from_float(0.85), el_from_float(0.9),
         "Canonical", tags)
     if !api_persisted(id) { return api_not_persisted(id) }
@@ -692,7 +740,7 @@ fn handle_api_link_entities(body: String) -> String {
     if is_protected_node(to_id) { return api_err_protected(to_id) }
     let relation: String = json_get(body, "relation")
     let eff_relation: String = if str_eq(relation, "") { "associates" } else { relation }
-    engram_connect(from_id, to_id, el_from_float(0.5), eff_relation)
+    wt_edge(from_id, to_id, el_from_float(0.5), eff_relation)
     return "{\"ok\":true,\"from_id\":\"" + from_id + "\",\"to_id\":\"" + to_id + "\",\"relation\":\"" + eff_relation + "\"}"
 }
 
@@ -725,11 +773,11 @@ fn handle_api_evolve_memory(body: String) -> String {
         }
     }
     let tags: String = "[\"Memory\",\"evolved\"]"
-    let new_id: String = engram_node_full(content, "Memory", "memory:evolved",
+    let new_id: String = wt_node(content, "Memory", "memory:evolved",
         sal, sal, el_from_float(0.9),
         "Episodic", tags)
     if !str_eq(prior_id, "") && !str_eq(new_id, "") {
-        engram_connect(new_id, prior_id, el_from_float(0.9), "supersedes")
+        wt_edge(new_id, prior_id, el_from_float(0.9), "supersedes")
     }
     return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\",\"ok\":true}"
 }
@@ -787,11 +835,11 @@ fn handle_api_cultivate(body: String) -> String {
         let content: String = json_get(body, "content")
         if str_eq(content, "") { return api_err("content is required") }
         let tags: String = "[\"Knowledge\",\"evolved\",\"cultivated\"]"
-        let new_id: String = engram_node_full(content, "Knowledge", "knowledge:cultivated",
+        let new_id: String = wt_node(content, "Knowledge", "knowledge:cultivated",
             el_from_float(0.75), el_from_float(0.75), el_from_float(0.9),
             "Episodic", tags)
         if !str_eq(prior_id, "") && !str_eq(new_id, "") {
-            engram_connect(new_id, prior_id, el_from_float(0.9), "supersedes")
+            wt_edge(new_id, prior_id, el_from_float(0.9), "supersedes")
         }
         return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\",\"ok\":true,\"cultivated\":true}"
     }
@@ -807,11 +855,11 @@ fn handle_api_cultivate(body: String) -> String {
             }
         }
         let tags: String = "[\"Memory\",\"evolved\",\"cultivated\"]"
-        let new_id: String = engram_node_full(content, "Memory", "memory:cultivated",
+        let new_id: String = wt_node(content, "Memory", "memory:cultivated",
             sal, sal, el_from_float(0.9),
             "Episodic", tags)
         if !str_eq(prior_id, "") && !str_eq(new_id, "") {
-            engram_connect(new_id, prior_id, el_from_float(0.9), "supersedes")
+            wt_edge(new_id, prior_id, el_from_float(0.9), "supersedes")
         }
         return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\",\"ok\":true,\"cultivated\":true}"
     }
@@ -831,7 +879,7 @@ fn handle_api_cultivate(body: String) -> String {
         if str_eq(to_id, "") { return api_err("to_id is required") }
         let relation: String = json_get(body, "relation")
         let eff_relation: String = if str_eq(relation, "") { "associates" } else { relation }
-        engram_connect(from_id, to_id, el_from_float(0.5), eff_relation)
+        wt_edge(from_id, to_id, el_from_float(0.5), eff_relation)
         return "{\"ok\":true,\"from_id\":\"" + from_id + "\",\"to_id\":\"" + to_id + "\",\"relation\":\"" + eff_relation + "\",\"cultivated\":true}"
     }
 
@@ -866,7 +914,7 @@ fn handle_api_consolidate(body: String) -> String {
     if !str_eq(summary, "") {
         let safe_summary: String = str_replace(summary, "\"", "'")
         let tags: String = "[\"SessionSummary\",\"consolidate\"]"
-        let summary_id: String = engram_node_full(
+        let summary_id: String = wt_node(
             "[session-summary] " + safe_summary,
             "SessionSummary", "session:summary",
             el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
@@ -878,3 +926,462 @@ fn handle_api_consolidate(body: String) -> String {
     }
     return "{\"ok\":true,\"snapshot\":\"" + snap + "\"}"
 }
+
+// ── Stage 1: structural audit ─────────────────────────────────────────────────
+//
+// WHAT THIS IMPLEMENTS
+//   The CGI provisional, 05-detailed-description.md, "Stage 1: Structural audit
+//   430". Verbatim, the audit module evaluates: the density and typed
+//   distribution of causal edges; the consistency between value nodes and
+//   execution-record neighborhoods; the richness and connectivity of the
+//   self-model; and the authenticity of open-question nodes in the wonder
+//   manifest. It "produces a coherence assessment 432 — NOT A BINARY SCORE but
+//   an annotated characterization of the graph's structural properties".
+//
+//   That last clause is the whole shape of this handler. Every finding carries
+//   its own numbers AND a plain-language note saying what the numbers mean and
+//   how they were obtained. There is no pass/fail, no percentage-of-health, no
+//   composite score, and `"score":null` is emitted explicitly so a downstream
+//   reader cannot mistake its absence for an omission.
+//
+// WHY IT EXISTS NOW, AND WHY THE FIRST FINDING IS THE ONE IT IS
+//   `runStructuralAudit` has been an advertised MCP tool with nothing behind it:
+//   the dispatcher GET'd /session/begin and returned that blob (mcp-wrapper/src/
+//   main.el). Meanwhile the failure the audit would have caught ran silently for
+//   about three weeks — the soul reported 103,089 nodes while the engram, which
+//   OWNS persistence, held ~79,900; a crash discarded the difference. Every boot
+//   reported green throughout, because nothing in the system ever compared the
+//   two sides. So finding 1 is owner-versus-runtime divergence: it is the check
+//   whose absence cost real memory, and it is cheap and exact.
+//
+// WHAT IS DELIBERATELY NOT HERE (stage 1b, see the `deferred` array in the
+// response): value/execution-record consistency and wonder-manifest
+// authenticity. Both need node types that barely exist in this graph today —
+// the response MEASURES those populations and reports the counts as the reason,
+// rather than asserting a deferral without evidence.
+//
+// MEASUREMENT HONESTY: EXACT WHERE CHEAP, SAMPLED WHERE NOT, ALWAYS LABELLED
+//   Counts, edge typing and self-model connectivity are exact. Orphan rate and
+//   dangling-edge rate are SAMPLED, because the engram runtime has no node-id
+//   index — `engram_find_node_index` is a linear scan over every node, so an
+//   exhaustive dangling check is O(nodes x edges) (~2.2e9 string compares at
+//   today's scale, tens of seconds inside one request). The samples are UNIFORM
+//   across the whole population, not head-of-list, and every sampled figure is
+//   emitted with its own `sampled` / `population` fields plus an extrapolation
+//   labelled as such. Raise `?edge_sample=` / `?node_sample=` to the population
+//   size to run either check exhaustively and pay the time. The real fix is an
+//   id index in the runtime; that is the engram repo's, not this handler's.
+
+// audit_pct1 — one-decimal percentage as a bare JSON number, sign-safe.
+// Integer math only: EL has no fixed-precision formatter, and float_to_str
+// would put an unbounded mantissa in the response.
+fn audit_pct1(num: Int, den: Int) -> String {
+    if den <= 0 { return "null" }
+    let neg: Bool = num < 0
+    let a: Int = if neg { 0 - num } else { num }
+    let tenths: Int = (a * 1000) / den
+    let whole: Int = tenths / 10
+    let frac: Int = tenths - (whole * 10)
+    let sign: String = if neg { "-" } else { "" }
+    return sign + int_to_str(whole) + "." + int_to_str(frac)
+}
+
+// audit_finding — the one envelope every finding uses: name, the measurements,
+// and the annotation. Keeping it in one place is what stops the characterization
+// from degenerating into a bag of numbers with no reading attached.
+fn audit_finding(name: String, measured: String, note: String) -> String {
+    return "{\"finding\":\"" + name + "\""
+        + ",\"measured\":{" + measured + "}"
+        + ",\"note\":\"" + api_json_escape(note) + "\"}"
+}
+
+// audit_str_at — read the quoted string value starting at byte `start`.
+// Slices a bounded window rather than the tail of the (multi-MB) edges array, so
+// this is O(window) per call instead of O(remaining input).
+fn audit_str_at(s: String, start: Int, maxlen: Int) -> String {
+    let n: Int = str_len(s)
+    if start < 0 || start >= n { return "" }
+    let end_guess: Int = start + maxlen
+    let stop: Int = if end_guess > n { n } else { end_guess }
+    let win: String = str_slice(s, start, stop)
+    let q: Int = str_index_of(win, "\"")
+    if q < 0 { return "" }
+    return str_slice(win, 0, q)
+}
+
+// audit_rel_count — exact count of edges carrying `rel`, by scanning the emitted
+// edge array for the literal `"relation":"<rel>"`. engram_emit_edge_json writes
+// metadata ESCAPED as a string, so no nested object can contain that literal and
+// the count cannot be inflated by edge payloads.
+fn audit_rel_count(edges: String, rel: String) -> Int {
+    return str_count(edges, "\"relation\":\"" + rel + "\"")
+}
+
+// audit_owner_stats — ask the persistence OWNER for its own counts.
+// Returns "" when there is no HTTP owner configured or the owner is unreachable;
+// both are reported as findings, never as a failure of the audit.
+fn audit_owner_stats(url: String) -> String {
+    if str_eq(url, "") { return "" }
+    return http_get(url + "/api/stats")
+}
+
+// audit_divergence — FINDING 1. Runtime (this soul's in-process graph) versus
+// the persistence owner's own count. Trend is measured against the previous
+// audit recorded in soul state, so a second call answers "is the gap growing?"
+// rather than just restating it.
+fn audit_divergence() -> String {
+    let rt_nodes: Int = engram_node_count()
+    let rt_edges: Int = engram_edge_count()
+    let url: String = wt_engram_url()
+
+    if str_eq(url, "") {
+        return audit_finding("owner_runtime_divergence",
+            "\"runtime_nodes\":" + int_to_str(rt_nodes)
+            + ",\"runtime_edges\":" + int_to_str(rt_edges)
+            + ",\"owner\":\"none\",\"owner_reachable\":false",
+            "No HTTP persistence owner is configured, so this soul IS the owner "
+            + "(file mode) and divergence is not defined. This check only has "
+            + "meaning when ENGRAM_URL points at a separate engram that owns the "
+            + "canonical store.")
+    }
+
+    let stats: String = audit_owner_stats(url)
+    // REACHABILITY IS PROVED BY THE PAYLOAD, NOT BY A NON-EMPTY REPLY.
+    // http_get does not return "" on a connection failure — it returns a JSON
+    // error object ({"error":"Failed to connect to ... Couldn't connect to
+    // server"}). Testing only for "" made a DEAD owner read as reachable with
+    // node_count 0, i.e. the audit would have reported a 100% divergence and
+    // named it as data loss. That false positive is worse than no check at all:
+    // it is precisely the kind of confident wrong answer this route exists to
+    // stop. Require the field the contract promises.
+    let owner_nc_raw: String = json_get_raw(stats, "node_count")
+    if str_eq(stats, "") || str_eq(owner_nc_raw, "") {
+        return audit_finding("owner_runtime_divergence",
+            "\"runtime_nodes\":" + int_to_str(rt_nodes)
+            + ",\"runtime_edges\":" + int_to_str(rt_edges)
+            + ",\"owner\":\"" + api_json_escape(url) + "\",\"owner_reachable\":false"
+            + ",\"owner_reply\":\"" + api_json_escape(api_utf8_trunc(stats, 200)) + "\"",
+            "The persistence owner at " + url + " did not return a node_count "
+            + "from GET /api/stats. Divergence is UNKNOWN, NOT ZERO — an owner "
+            + "that cannot be read is exactly the condition under which the "
+            + "runtime's own count means least, and reporting 0 for the owner "
+            + "would manufacture a total-loss reading out of a network error. "
+            + "Reported as a finding rather than raised as an error so the rest "
+            + "of the audit still returns; the owner's raw reply is in "
+            + "owner_reply.")
+    }
+
+    let ow_nodes: Int = json_get_int(stats, "node_count")
+    let ow_edges: Int = json_get_int(stats, "edge_count")
+    let d_nodes: Int = rt_nodes - ow_nodes
+    let d_edges: Int = rt_edges - ow_edges
+
+    // Trend against the previous audit in this soul's state.
+    let prev_raw: String = state_get("audit_prev_node_delta")
+    let prev: Int = str_to_int(prev_raw)
+    let abs_now: Int = if d_nodes < 0 { 0 - d_nodes } else { d_nodes }
+    let abs_prev: Int = if prev < 0 { 0 - prev } else { prev }
+    let trend: String = if str_eq(prev_raw, "") {
+        "no_prior_audit"
+    } else {
+        if abs_now > abs_prev { "growing" } else {
+            if abs_now < abs_prev { "shrinking" } else { "flat" }
+        }
+    }
+    state_set("audit_prev_node_delta", int_to_str(d_nodes))
+    state_set("audit_prev_ts", int_to_str(time_now()))
+
+    let note_head: String = if d_nodes == 0 {
+        "Runtime and owner agree on node count."
+    } else {
+        "Runtime holds " + int_to_str(d_nodes) + " nodes (" + audit_pct1(d_nodes, rt_nodes)
+        + "% of its own graph) that the persistence owner does not report. Nodes "
+        + "that exist only in runtime memory do not survive a restart."
+    }
+    return audit_finding("owner_runtime_divergence",
+        "\"runtime_nodes\":" + int_to_str(rt_nodes)
+        + ",\"runtime_edges\":" + int_to_str(rt_edges)
+        + ",\"owner\":\"" + api_json_escape(url) + "\",\"owner_reachable\":true"
+        + ",\"owner_nodes\":" + int_to_str(ow_nodes)
+        + ",\"owner_edges\":" + int_to_str(ow_edges)
+        + ",\"node_delta\":" + int_to_str(d_nodes)
+        + ",\"edge_delta\":" + int_to_str(d_edges)
+        + ",\"node_delta_pct_of_runtime\":" + audit_pct1(d_nodes, rt_nodes)
+        + ",\"trend_vs_previous_audit\":\"" + trend + "\""
+        + ",\"previous_node_delta\":" + (if str_eq(prev_raw, "") { "null" } else { int_to_str(prev) }),
+        note_head + " Trend against the previous audit recorded in this soul's "
+        + "state: " + trend + ". This is the comparison whose absence let a "
+        + "~24,000-node loss run for weeks with every boot reporting green.")
+}
+
+// audit_edge_typing — FINDING 2. Density plus the typed distribution the patent
+// asks for, against the claim-10 relation vocabulary. Exact: str_count over the
+// emitted edge array, one linear pass per relation.
+fn audit_edge_typing(edges: String, total_edges: Int, node_total: Int) -> String {
+    let c_sup: Int = audit_rel_count(edges, "Supersedes")
+    let c_cau: Int = audit_rel_count(edges, "Causes")
+    let c_con: Int = audit_rel_count(edges, "Contains")
+    let c_ref: Int = audit_rel_count(edges, "References")
+    let c_ctr: Int = audit_rel_count(edges, "Contradicts")
+    let c_exe: Int = audit_rel_count(edges, "Exemplifies")
+    let c_act: Int = audit_rel_count(edges, "Activates")
+    let c_tmp: Int = audit_rel_count(edges, "TemporallyPrecedes")
+    let typed: Int = c_sup + c_cau + c_con + c_ref + c_ctr + c_exe + c_act + c_tmp
+
+    // Lowercase near-misses: the same eight concepts written by the ad-hoc write
+    // paths (linkEntities defaults to "associates", linkCausal to "causes").
+    // Counted separately because "the vocabulary is unused" and "the vocabulary
+    // is used in the wrong case" are different defects with different fixes.
+    let l_sup: Int = audit_rel_count(edges, "supersedes")
+    let l_cau: Int = audit_rel_count(edges, "causes")
+    let l_con: Int = audit_rel_count(edges, "contains")
+    let l_ref: Int = audit_rel_count(edges, "references")
+    let l_ctr: Int = audit_rel_count(edges, "contradicts")
+    let l_exe: Int = audit_rel_count(edges, "exemplifies")
+    let l_act: Int = audit_rel_count(edges, "activates")
+    let l_tmp: Int = audit_rel_count(edges, "temporallyPrecedes")
+    let near: Int = l_sup + l_cau + l_con + l_ref + l_ctr + l_exe + l_act + l_tmp
+
+    let untyped: Int = total_edges - typed
+    return audit_finding("typed_edge_distribution",
+        "\"total_edges\":" + int_to_str(total_edges)
+        + ",\"total_nodes\":" + int_to_str(node_total)
+        // Density per 100 nodes, not per node: EL has no fixed-precision float
+        // formatter, and "0.3 edges per node" rounded to an integer is a lie.
+        + ",\"edges_per_100_nodes\":" + audit_pct1(total_edges, node_total)
+        + ",\"claim10_typed\":" + int_to_str(typed)
+        + ",\"claim10_typed_pct\":" + audit_pct1(typed, total_edges)
+        + ",\"outside_claim10_vocabulary\":" + int_to_str(untyped)
+        + ",\"lowercase_near_miss\":" + int_to_str(near)
+        + ",\"by_relation\":{"
+        + "\"Supersedes\":" + int_to_str(c_sup)
+        + ",\"Causes\":" + int_to_str(c_cau)
+        + ",\"Contains\":" + int_to_str(c_con)
+        + ",\"References\":" + int_to_str(c_ref)
+        + ",\"Contradicts\":" + int_to_str(c_ctr)
+        + ",\"Exemplifies\":" + int_to_str(c_exe)
+        + ",\"Activates\":" + int_to_str(c_act)
+        + ",\"TemporallyPrecedes\":" + int_to_str(c_tmp) + "}",
+        "Only " + int_to_str(typed) + " of " + int_to_str(total_edges)
+        + " edges use the claim-10 causal vocabulary; the remainder are ad-hoc "
+        + "relation strings, which is why the graph's causal claims cannot yet "
+        + "be checked for internal consistency — an untyped edge asserts "
+        + "association, not causation. " + int_to_str(near) + " edges use a "
+        + "lowercase spelling of a claim-10 relation: those are near-misses the "
+        + "write paths could be corrected to emit, not genuinely foreign types.")
+}
+
+// audit_orphans_dangling — FINDING 3. Both figures are SAMPLED; see the header
+// for why exhaustive is O(nodes x edges) on this runtime.
+//
+// An "orphan" here is a node with zero RESOLVABLE edges: engram_neighbors_json
+// drops any edge whose other endpoint does not resolve to a node, so a node
+// whose only edges are dangling reads as an orphan. That is the right reading —
+// such a node is unreachable by traversal — but it is stated rather than hidden.
+fn audit_orphans_dangling(edges: String, total_edges: Int, node_total: Int,
+                          edge_cap: Int, node_cap: Int) -> String {
+    // ── orphan sample: uniform stride over the node store ──
+    let n_take: Int = if node_total < node_cap { node_total } else { node_cap }
+    let n_stride: Int = if n_take > 0 { node_total / n_take } else { 1 }
+    let n_stride = if n_stride < 1 { 1 } else { n_stride }
+    let orphans: Int = 0
+    let n_checked: Int = 0
+    let j: Int = 0
+    while j < n_take {
+        let one: String = engram_scan_nodes_json(1, j * n_stride)
+        let nid: String = json_get(json_array_get(one, 0), "id")
+        if !str_eq(nid, "") {
+            let nbrs: String = engram_neighbors_json(nid, 1, "both")
+            let deg: Int = json_array_len(nbrs)
+            let orphans = if deg == 0 { orphans + 1 } else { orphans }
+            let n_checked = n_checked + 1
+        }
+        let j = j + 1
+    }
+
+    // ── dangling sample: uniform stride over the edge array ──
+    // str_index_of_all gives every edge's field offsets in ONE linear pass, so
+    // any index can be read in O(1). json_array_get would have been O(i) per
+    // element and O(n^2) over the array.
+    let from_pos: [Int] = str_index_of_all(edges, "\"from_id\":\"")
+    let to_pos: [Int] = str_index_of_all(edges, "\"to_id\":\"")
+    let nf: Int = len(from_pos)
+    let nt: Int = len(to_pos)
+    let ne: Int = if nf < nt { nf } else { nt }
+    let e_take: Int = if ne < edge_cap { ne } else { edge_cap }
+    let e_stride: Int = if e_take > 0 { ne / e_take } else { 1 }
+    let e_stride = if e_stride < 1 { 1 } else { e_stride }
+    let dangling: Int = 0
+    let e_checked: Int = 0
+    let i: Int = 0
+    while i < ne && e_checked < e_take {
+        let fid: String = audit_str_at(edges, get(from_pos, i) + 11, 96)
+        let tid: String = audit_str_at(edges, get(to_pos, i) + 9, 96)
+        let f_gone: Bool = str_eq(engram_get_node_json(fid), "{}")
+        let t_gone: Bool = if f_gone { true } else { str_eq(engram_get_node_json(tid), "{}") }
+        let dangling = if f_gone || t_gone { dangling + 1 } else { dangling }
+        let e_checked = e_checked + 1
+        let i = i + e_stride
+    }
+
+    let orphan_est: Int = if n_checked > 0 { (orphans * node_total) / n_checked } else { 0 }
+    let dangle_est: Int = if e_checked > 0 { (dangling * total_edges) / e_checked } else { 0 }
+    let exhaustive_n: String = if n_checked >= node_total { "true" } else { "false" }
+    let exhaustive_e: String = if e_checked >= ne { "true" } else { "false" }
+
+    return audit_finding("orphans_and_dangling_edges",
+        "\"nodes_population\":" + int_to_str(node_total)
+        + ",\"nodes_sampled\":" + int_to_str(n_checked)
+        + ",\"nodes_sample_exhaustive\":" + exhaustive_n
+        + ",\"orphans_in_sample\":" + int_to_str(orphans)
+        + ",\"orphan_rate_pct\":" + audit_pct1(orphans, n_checked)
+        + ",\"orphans_extrapolated\":" + int_to_str(orphan_est)
+        + ",\"edges_population\":" + int_to_str(total_edges)
+        + ",\"edges_sampled\":" + int_to_str(e_checked)
+        + ",\"edges_sample_exhaustive\":" + exhaustive_e
+        + ",\"dangling_in_sample\":" + int_to_str(dangling)
+        + ",\"dangling_rate_pct\":" + audit_pct1(dangling, e_checked)
+        + ",\"dangling_extrapolated\":" + int_to_str(dangle_est),
+        "Orphan = zero RESOLVABLE edges, so a node whose only edges dangle counts "
+        + "as an orphan; either way it is unreachable by traversal. Dangling = an "
+        + "edge with an endpoint id that resolves to no node. Both are uniform "
+        + "stride samples over the whole population, not the head of the list; "
+        + "the extrapolations are estimates and are labelled as such. Pass "
+        + "?node_sample= / ?edge_sample= at or above the population size to run "
+        + "either check exhaustively. A high orphan rate is a characterization, "
+        + "not a verdict: an accumulating store legitimately holds unlinked "
+        + "material. It becomes a defect when the write paths were SUPPOSED to "
+        + "link and did not.")
+}
+
+// audit_pillar — one self-model pillar: present, how much content, how connected.
+fn audit_pillar(key: String, id: String) -> String {
+    let node: String = engram_get_node_json(id)
+    let present: Bool = !str_eq(node, "{}") && !str_eq(node, "")
+    if !present {
+        return "\"" + key + "\":{\"id\":\"" + id + "\",\"present\":false"
+            + ",\"content_length\":0,\"degree\":0}"
+    }
+    let content: String = json_get(node, "content")
+    let deg: Int = json_array_len(engram_neighbors_json(id, 1, "both"))
+    return "\"" + key + "\":{\"id\":\"" + id + "\",\"present\":true"
+        + ",\"label\":\"" + api_json_escape(json_get(node, "label")) + "\""
+        + ",\"tier\":\"" + api_json_escape(json_get(node, "tier")) + "\""
+        + ",\"content_length\":" + int_to_str(str_len(content))
+        + ",\"degree\":" + int_to_str(deg) + "}"
+}
+
+// audit_self_model — FINDING 4. "the richness and connectivity of the
+// self-model ... is it connected to behavioral evidence?"
+//
+// This finding RETIRES the Claude-side vitals identity block. That check lived
+// outside the system it was checking — a shell script grepping a snapshot — so
+// it could only ever report on a file, and it went on reporting green while the
+// memory-philosophy pillar was absent from the live graph for about three weeks.
+// Asking the running soul about its own three pillars is the designed mechanism;
+// a shell probe was the fourth patch on the same hole.
+fn audit_self_model() -> String {
+    let dna: String = audit_pillar("intellectual_dna", "kn-5adecd7e-d6db-4576-87fe-6ef8a935cea6")
+    let val: String = audit_pillar("values_hub", "kn-5b606390-a52d-4ca2-8e0e-eba141d13440")
+    let phi: String = audit_pillar("memory_philosophy", "kn-dcfe04b3-3702-4cac-b6f0-ecb4db837eee")
+    let root: String = audit_pillar("self_root", "kn-efeb4a5b-5aff-4759-8a97-7233099be6ee")
+    return audit_finding("self_model_connectivity",
+        "\"pillars\":{" + dna + "," + val + "," + phi + "," + root + "}",
+        "The three identity pillars plus the self root. `degree` counts nodes "
+        + "reachable in one hop in either direction — the self-model's connection "
+        + "to the rest of the graph. present:false on any pillar is the condition "
+        + "that ran undetected for weeks; content_length distinguishes a pillar "
+        + "that is present from one that is present but hollowed out. The patent "
+        + "also asks whether the self-model makes ACCURATE PREDICTIONS about the "
+        + "system's own behavior; that half needs Prediction nodes and is deferred "
+        + "with the rest of stage 1b below.")
+}
+
+// audit_deferred — what stage 1 does NOT yet evaluate, with the measured reason.
+// Emitted as data, not as a comment, so a reader of the assessment sees the gap
+// and its evidence rather than inferring completeness from silence.
+fn audit_deferred() -> String {
+    let preds: Int = json_array_len(api_or_empty(engram_scan_nodes_by_type_json("Prediction", 50, 0)))
+    let wonders: Int = json_array_len(api_or_empty(engram_scan_nodes_by_type_json("WonderQuestion", 50, 0)))
+    return "[{\"deferred\":\"value_execution_record_consistency\""
+        + ",\"stage\":\"1b\""
+        + ",\"measured\":{\"prediction_nodes_found\":" + int_to_str(preds) + "}"
+        + ",\"reason\":\"" + api_json_escape(
+            "The patent asks whether the execution history SUPPORTS the stated "
+            + "values or shows systematic conflict. That requires execution "
+            + "records tied to value nodes and predictions to score them against. "
+            + "Prediction nodes found (capped at 50): " + int_to_str(preds)
+            + ". Asserting value/execution coherence on that population would be "
+            + "a fabricated result, which is worse than a stated gap.") + "\"}"
+        + ",{\"deferred\":\"wonder_manifest_authenticity\""
+        + ",\"stage\":\"1b\""
+        + ",\"measured\":{\"wonder_question_nodes_found\":" + int_to_str(wonders) + "}"
+        + ",\"reason\":\"" + api_json_escape(
+            "The patent asks whether pull weights CORRELATE WITH GENUINE "
+            + "PREDICTION UNCERTAINTY or are uniform/externally assigned — a "
+            + "correlation between two populations. WonderQuestion nodes readable "
+            + "by type (capped at 50): " + int_to_str(wonders) + ", against "
+            + int_to_str(preds) + " Prediction nodes. There is a known write/read "
+            + "node-type mismatch on the wonder path; until that is fixed and both "
+            + "populations exist, any correlation reported here would be noise.") + "\"}]"
+}
+
+// handle_api_structural_audit — Stage 1. Returns the coherence assessment 432:
+// an annotated characterization, explicitly NOT a score.
+//
+// COST NOTE: the edge findings need the relation labels, and the runtime exposes
+// no edge-enumeration builtin. The only way to see them is the same one
+// GET /api/graph/edges already uses — engram_save to a SCRATCH path (never the
+// owner's canonical file; see routes.el, neuron#117) and read the array back.
+// On a large graph that is a multi-hundred-MB write, so this is a manual audit
+// route, not something to put on a timer. Pass ?edges=0 to skip both edge
+// findings and get the divergence + self-model readings cheaply.
+fn handle_api_structural_audit(method: String, path: String, body: String) -> String {
+    let node_total: Int = engram_node_count()
+    let edge_total: Int = engram_edge_count()
+    let want_edges: Bool = !str_eq(api_query_param(path, "edges"), "0")
+    let edge_cap: Int = api_query_int(path, "edge_sample", 3000)
+    let node_cap: Int = api_query_int(path, "node_sample", 300)
+
+    let divergence: String = audit_divergence()
+    let self_model: String = audit_self_model()
+
+    let edge_part: String = if want_edges {
+        // Scratch export only. state_get("soul_snapshot_path") is deliberately
+        // NOT used: in HTTP-engram mode the soul is not the persistence owner and
+        // must never write the canonical file, not even on a read path.
+        let scratch_dir: String = env("TMPDIR")
+        let scratch_base: String = if str_eq(scratch_dir, "") { "/tmp" } else { scratch_dir }
+        let snap_path: String = scratch_base + "/soul-audit-export-" + state_get("soul_cgi_id") + ".json"
+        // engram_save returns Int (1 ok / 0 fail); str_eq on it SIGSEGVs (#150).
+        let saved: Int = engram_save(snap_path)
+        if saved == 0 {
+            "," + audit_finding("typed_edge_distribution", "\"available\":false",
+                "Could not export the graph to " + snap_path + " for edge analysis, "
+                + "so edge typing and the dangling-edge sample were not run. "
+                + "Reported as a gap, not as zero findings.")
+        } else {
+            // wt_read, not fs_read: fs_read leaves a thread-local length hint that
+            // the NEXT HTTP response would use as its Content-Length, appending
+            // adjacent heap bytes to the reply (see persist.el wt_read).
+            let snap: String = wt_read(snap_path)
+            let edges_raw: String = json_get_raw(snap, "edges")
+            let edges: String = if str_eq(edges_raw, "") { "[]" } else { edges_raw }
+            "," + audit_edge_typing(edges, edge_total, node_total)
+            + "," + audit_orphans_dangling(edges, edge_total, node_total, edge_cap, node_cap)
+        }
+    } else {
+        ""
+    }
+
+    return "{\"audit\":\"structural\",\"stage\":1"
+        + ",\"spec\":\"CGI provisional 05-detailed-description.md, Stage 1: Structural audit 430\""
+        + ",\"assessment\":\"coherence_assessment_432\""
+        + ",\"assessment_kind\":\"annotated_characterization\""
+        + ",\"score\":null"
+        + ",\"score_note\":\"By design. The specification calls for an annotated characterization of the graph's structural properties, not a binary score. Read the findings.\""
+        + ",\"cgi_id\":\"" + api_json_escape(state_get("soul_cgi_id")) + "\""
+        + ",\"ts_ms\":" + int_to_str(time_now())
+        + ",\"findings\":[" + divergence + "," + self_model + edge_part + "]"
+        + ",\"deferred\":" + audit_deferred() + "}"
+}

neuron-api.elh

@@ -37,3 +37,4 @@ extern fn handle_api_memory_update(body: String) -> String
 extern fn handle_api_cultivate(body: String) -> String
 extern fn handle_api_list_typed(node_type: String, path: String, body: String) -> String
 extern fn handle_api_consolidate(body: String) -> String
+extern fn handle_api_structural_audit(method: String, path: String, body: String) -> String

neuron-dev-setup/README.md

@@ -0,0 +1,171 @@
+# neuron-dev-setup — one-command Neuron CORE dev stack
+
+Stand up an identical **Neuron brain + agent** on a fresh Mac so any developer
+gets the same local runtime to build against. This is the **CORE** dev stack
+only — the four native `launchd` services that make Neuron think, remember, and
+speak MCP to Claude Code. Will's personal automations (catalyst, telegram,
+vessels, studio, self-review, world-integrator, council, compressor, snapshots,
+act-runner, …) are **deliberately excluded**.
+
+```
+  ┌─────────────┐        ┌──────────────┐
+  │  soul :7770 │ ─────► │ engram :8742 │     the mind ──► its memory substrate
+  └─────────────┘        └──────────────┘
+        ▲
+        │
+  ┌───────────────────┐
+  │ mcp-wrapper :17779│  ─── MCP surface over the soul HTTP API (internal)
+  └───────────────────┘
+        ▲
+        │
+  ┌────────────────┐
+  │ mcp-proxy :7779│  ◄─── Claude Code connects here (stable front door)
+  └────────────────┘
+```
+
+Claude Code's `neuron` MCP server points at `http://127.0.0.1:7779/` — the proxy.
+The proxy forwards to the wrapper (`:17779`), which calls the soul (`:7770`),
+which reads/writes the engram (`:8742`). The engram is the persistent brain.
+
+## Quick start
+
+```bash
+git clone <this-repo> && cd neuron-dev-setup
+cp config.env.example config.env      # optional — edit ports/paths if you like
+./install.sh                          # prompts for your Anthropic API key
+```
+
+Then verify:
+
+```bash
+curl http://localhost:8742/health     # engram
+curl http://localhost:7770/health         # soul
+curl http://localhost:7779/health         # mcp-proxy (what Claude Code uses)
+launchctl list | grep ai.neuron
+```
+
+Open Claude Code — the `neuron` MCP tools should be live, backed by **your own**
+local brain. `./install.sh --dry-run` shows every action without touching anything.
+
+## What the installer does (8 phases)
+
+| Phase | Action |
+|------|--------|
+| 1 | Preflight: macOS/arm64, ensure `git cc curl python3` + `openssl@3` (via Homebrew) |
+| 2 | Prompt for the **Anthropic API key**, store it in the **macOS Keychain** (never a file) |
+| 3 | Clone `neuron`, `engram`, `foundation`; fetch the El toolchain; build 4 binaries + `forge` |
+| 4 | Lay down `~/.neuron/{bin,logs,engram}` and the templated `soul-wrapper.sh` |
+| 5 | Generate + load the 4 core LaunchAgents (engram → soul → wrapper → proxy) |
+| 6 | Seed a fresh engram with the **genesis identity** via `forge install` |
+| 7 | Install Claude config: `neuron` agent, core hooks, local MCP registration |
+| 8 | Health-check all four ports |
+
+Everything is **idempotent** (safe to re-run) and **templated** to the invoking
+user's `$HOME` — no path is hardcoded to another machine.
+
+## Prerequisites
+
+- macOS on Apple Silicon (uses `launchd`; soul build flags assume arm64).
+- **Xcode Command Line Tools** (`xcode-select --install`) — provides `cc`, `git`.
+- **Homebrew** — for `openssl@3`, `curl`.
+- An **Anthropic API key** — the soul's inference provider. Prompted for; stored
+  in Keychain under service `neuron-llm-0-key`; read at launch by `soul-wrapper.sh`.
+- **Git access** to Gitea (`git.neuralplatform.ai`) for the source repos.
+- **GCP access** to project `neuron-785695` Artifact Registry (default El
+  toolchain source). Ask Will to grant it, or set `EL_TOOLCHAIN_SOURCE=local`.
+
+## Core-stack map (what gets replicated)
+
+| Service | Port | Binary | Built from | LaunchAgent |
+|---------|------|--------|------------|-------------|
+| soul | 7770 | `neuron/dist/neuron` | `dist/soul.c` + El runtime, `cc` (CI recipe) | `ai.neuron.soul` |
+| engram | 8742 | `engram/dist/engram` | `engram` repo `src/server.el` via `elc`→`cc` | `ai.neuron.engram` |
+| mcp-wrapper | 17779 | `neuron/mcp-wrapper/dist/neuron-mcp-wrapper` | `mcp-wrapper/src/main.el` | `ai.neuron.mcp-wrapper` |
+| mcp-proxy | 7779 | `neuron/mcp-proxy/dist/neuron-mcp-proxy` | `mcp-proxy/src/main.el` | `ai.neuron.mcp-proxy` |
+
+**`~/.neuron` layout the installer creates**
+
+```
+~/.neuron/
+  bin/soul-wrapper.sh     # reads Anthropic key from Keychain, execs the soul binary
+  logs/                   # soul.*.log, engram.log, mcp-*.log
+  engram/                 # ENGRAM_DATA_DIR — the persistent brain (snapshot.json + db)
+```
+
+**Identity seed.** `foundation/forge/seeds/neuron-genesis-seed.json` carries
+`identity_nodes[]` + `edges[]` with **fixed** knowledge-node IDs (e.g.
+`kn-efeb4a5b-5aff-4759-8a97-7233099be6ee`, the "self" traversal root). Those exact
+IDs are referenced by the SessionStart self-load hook and the neuron agent, so
+seeding must **preserve IDs** — `forge install <seed>` is the mechanism.
+
+**Claude config installed** (`~/.claude/`)
+
+- `agents/neuron.md` — the Neuron agent (identity, session protocol, five primitives).
+- `mcp.json` — registers `neuron` → `http://127.0.0.1:7779/`.
+- `settings.json` hooks (CORE subset only):
+  - `SessionStart` → `neuron-self-load.sh` (loads identity from the seeded engram)
+  - `PreToolUse:Agent` → `neuron-agent-preamble.sh` (subagents load substrate first)
+  - `PreCompact` → `pre-compact.sh` (clean context recovery)
+
+### Deliberately EXCLUDED from core
+
+- **`check-active-contexts.sh`** and **`require-execution-context.sh`** — these
+  depend on a separate filesystem repo `~/Development/projects/active/neuron/synapse`.
+  `require-execution-context.sh` is a hard `Edit/Write` gate that would **block a
+  fresh dev from editing any file** without that synapse repo. Not core; excluded.
+- `engram-mirror.py` (PostToolUse) — optional; mirrors MCP writes to engram.
+- All Will-personal LaunchAgents: `catalyst-*`, `telegram-gateway`, `vessel.*`,
+  `studio`, `self-review`, `world-integrator`, `council`, `compressor`,
+  `cultivation-digest`, `snapshot-backup`, `engram-backup`, `act-runner`, `keymap`,
+  `invest`, and the disabled `ai.neuron.api` (`:7771` is a personal Python
+  perception helper — confirmed not core).
+
+## Secrets — how they're handled
+
+- **Anthropic key**: prompted for; stored in Keychain; read at launch. Never in a
+  plist, this repo, or a log.
+- **Engram local token** (`ENGRAM_API_KEY`): a *loopback-only* dev token, not a
+  cloud secret. Defaults to a generated `ntn-dev-*` value; override in `config.env`.
+- No cloud tokens, Vault tokens, CF-Access secrets, or founder keys are copied.
+  (Will's live `start-daemon.sh`/`neuron-api-launch.sh` contain such keys — this
+  installer intentionally does **not** use those files.)
+
+## Uninstall
+
+```bash
+./uninstall.sh                # stop + remove the 4 LaunchAgents and added Claude hooks
+./uninstall.sh --purge-data   # ALSO delete ~/.neuron/engram (destroys the brain)
+```
+
+## OPEN QUESTIONS (need Will to confirm)
+
+1. **El toolchain acquisition.** The default path fetches `el-runtime-c/-h` and
+   `el-elc` from GCP Artifact Registry (mirrors `neuron/.gitea/workflows/ci.yaml`).
+   A new dev needs GCP access to `neuron-785695`. Is that the intended path, or
+   should the El SDK be published/vendored for onboarding?
+2. **`elc` invocation for engram/wrapper/proxy.** The soul build (`cc dist/soul.c
+   + el_runtime.c`) is verified from CI. The `.el → .c` transpile step for engram,
+   mcp-wrapper, and mcp-proxy is inferred (`elc <src> -o <out.c>`). Confirm the
+   exact flags / entrypoints (CI notes `elb` OOMs on Linux; macOS builds differ).
+3. **`forge install` ID preservation.** Confirm `forge install` writes the seed's
+   fixed `kn-` IDs verbatim (the self-load hook hardcodes `kn-efeb4a5b…`). If it
+   re-mints IDs, the hook + agent identity load would break on a fresh brain.
+4. **engram repo layout.** The live engram binary is built from `src/server.el`
+   (Gitea repo `neuron-technologies/engram`, cloned in CI). Confirm that repo is
+   the canonical source for onboarding (the local `foundation/el/engram` copy has
+   the same `src/server.el`).
+5. **Home for this bundle** — see below.
+
+## Where this should live (recommendation)
+
+**Recommendation: a dedicated `neuron-dev-setup` (or `neuron-onboarding`) repo —
+NOT `neuron-code`.** `neuron-code` already exists as a real product ("Neuron Code",
+a coding tool with `nc-cli` + vessels — local `products/neuron-code` has commits);
+repurposing it for onboarding would collide with a shipped product's identity.
+
+This bundle was scaffolded as `neuron-dev-setup/` on branch `feat/neuron-dev-setup`
+in the **`neuron` repo** (off `origin/main`) and opened as a PR for review, because
+the neuron repo already hosts the soul source, the verified CI build recipe, and
+the mcp-wrapper/proxy sources — the natural review surface. If you'd rather it be
+its own repo, move this directory into a fresh `neuron-dev-setup` repo verbatim;
+nothing here depends on living inside the neuron repo.

neuron-dev-setup/config.env.example

@@ -0,0 +1,45 @@
+# neuron-dev-setup — configuration
+# Copy to  config.env  and edit if you want non-default paths/ports.
+# install.sh sources this file if it exists; otherwise it uses these defaults.
+# NOTHING here is a secret. The Anthropic API key is read from your Keychain,
+# never from this file. See README.md.
+
+# ── Where the core stack lives ────────────────────────────────────────────────
+# All paths are relative to your own $HOME — never hardcode another user's home.
+NEURON_HOME="${HOME}/.neuron"                       # runtime home: bin/, logs/, engram data
+DEV_ROOT="${HOME}/Development/neuron-technologies"   # where source repos are cloned/built
+
+# ── Git remotes (Gitea is primary) ───────────────────────────────────────────
+GITEA_BASE="git@git.neuralplatform.ai:neuron-technologies"
+NEURON_REPO_URL="${GITEA_BASE}/neuron.git"          # soul + mcp-wrapper + mcp-proxy source
+ENGRAM_REPO_URL="${GITEA_BASE}/engram.git"          # engram memory substrate
+# NOTE: there is no foundation.git repo. The El toolchain is fetched via
+# EL_TOOLCHAIN_SOURCE below; the forge seed installer is optional (Phase 6).
+NEURON_REPO_BRANCH="main"
+
+# ── Ports (must match across services; change only if a port clashes) ─────────
+SOUL_PORT="7770"        # soul daemon HTTP API
+ENGRAM_PORT="8742"      # engram memory substrate
+WRAPPER_PORT="17779"    # mcp-wrapper (internal, talks to soul)
+PROXY_PORT="7779"       # mcp-proxy (stable front door Claude Code connects to)
+
+# ── Engram ────────────────────────────────────────────────────────────────────
+ENGRAM_DATA_DIR="${NEURON_HOME}/engram"
+# Local shared auth token for the engram/soul HTTP APIs on loopback. This is a
+# LOCAL dev token (not a cloud secret); override it if you like. install.sh will
+# generate a random one if you leave it empty.
+ENGRAM_API_KEY="ntn-dev-local"
+
+# ── El toolchain source (needed to build engram / mcp-wrapper / mcp-proxy) ────
+# Option A (default): fetch prebuilt El runtime + elc from GCP Artifact Registry
+#   (requires `gcloud auth` with access to project neuron-785695 — ask Will).
+#   Without gcloud the installer skips the El-dependent builds and still completes.
+# Option B: use a prebuilt El toolchain (elc + el_runtime.{c,h}) you have already
+#   staged in ${DEV_ROOT}/.el-runtime.
+EL_TOOLCHAIN_SOURCE="artifact-registry"   # artifact-registry | local
+GCP_PROJECT="neuron-785695"
+GCP_AR_REPO="foundation-prod"
+GCP_AR_LOCATION="us-central1"
+
+# ── Keychain service name for the Anthropic key (read by soul-wrapper.sh) ─────
+KEYCHAIN_SERVICE="neuron-llm-0-key"

neuron-dev-setup/install.sh

@@ -0,0 +1,441 @@
+#!/usr/bin/env bash
+#
+# neuron-dev-setup / install.sh
+# ─────────────────────────────────────────────────────────────────────────────
+# One-command onboarding for the Neuron CORE dev stack on a fresh Mac.
+#
+# Stands up, as native launchd services, the four processes a developer needs to
+# have an identical "Neuron brain + agent" to build against:
+#
+#     soul  (:7770)  ──►  engram (:8742)        the mind + its memory substrate
+#       ▲                     ▲
+#       │                     │
+#   mcp-wrapper (:17779) ──►  soul              MCP surface over the soul API
+#       ▲
+#       │
+#   mcp-proxy   (:7779)  ◄── Claude Code        stable MCP front door
+#
+# It also seeds a fresh engram with Neuron's identity (the genesis seed) and lays
+# down the Claude Code config (neuron agent + core hooks + local MCP registration)
+# so a new dev's `claude` talks to *their own* local Neuron.
+#
+# DESIGN RULES
+#   * Idempotent: safe to re-run. Existing state is detected and reused.
+#   * Templated: every path/port/user is derived from $HOME and config.env.
+#     Nothing is hardcoded to another developer's machine.
+#   * Secret-free: the Anthropic key is prompted for and stored in the macOS
+#     Keychain. No key is ever written to a plist, this repo, or a logfile.
+#
+# USAGE
+#   ./install.sh                 # full install
+#   ./install.sh --dry-run       # print what would happen, touch nothing
+#   ./install.sh --skip-build    # assume binaries already built (see --use-local)
+#   ./install.sh --skip-services # lay down files but don't load LaunchAgents
+#   ./install.sh --help
+# ─────────────────────────────────────────────────────────────────────────────
+set -euo pipefail
+
+# ── Locate ourselves ─────────────────────────────────────────────────────────
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+TEMPLATES="${SCRIPT_DIR}/templates"
+
+# ── Flags ────────────────────────────────────────────────────────────────────
+DRY_RUN=0; SKIP_BUILD=0; SKIP_SERVICES=0; USE_LOCAL_BINARIES=0
+for arg in "$@"; do
+  case "$arg" in
+    --dry-run)       DRY_RUN=1 ;;
+    --skip-build)    SKIP_BUILD=1 ;;
+    --skip-services) SKIP_SERVICES=1 ;;
+    --use-local)     USE_LOCAL_BINARIES=1 ;;
+    --help|-h)
+      sed -n '2,40p' "${BASH_SOURCE[0]}" | sed 's/^# \{0,1\}//'
+      exit 0 ;;
+    *) echo "unknown flag: $arg" >&2; exit 2 ;;
+  esac
+done
+
+# ── Pretty logging ───────────────────────────────────────────────────────────
+c_blue=$'\033[1;34m'; c_grn=$'\033[1;32m'; c_yel=$'\033[1;33m'; c_red=$'\033[1;31m'; c_off=$'\033[0m'
+step() { echo "${c_blue}▶${c_off} $*"; }
+ok()   { echo "${c_grn}✓${c_off} $*"; }
+warn() { echo "${c_yel}!${c_off} $*"; }
+die()  { echo "${c_red}✗ $*${c_off}" >&2; exit 1; }
+run()  { if [ "$DRY_RUN" = 1 ]; then echo "   [dry-run] $*"; else eval "$*"; fi; }
+
+# ── Load config ──────────────────────────────────────────────────────────────
+if [ -f "${SCRIPT_DIR}/config.env" ]; then
+  # shellcheck disable=SC1091
+  source "${SCRIPT_DIR}/config.env"
+else
+  # shellcheck disable=SC1091
+  source "${SCRIPT_DIR}/config.env.example"
+  warn "No config.env found — using defaults from config.env.example."
+fi
+
+# Derived / defaulted values (never hardcode a home directory)
+: "${NEURON_HOME:=${HOME}/.neuron}"
+: "${DEV_ROOT:=${HOME}/Development/neuron-technologies}"
+: "${SOUL_PORT:=7770}"; : "${ENGRAM_PORT:=8742}"; : "${WRAPPER_PORT:=17779}"; : "${PROXY_PORT:=7779}"
+: "${ENGRAM_DATA_DIR:=${NEURON_HOME}/engram}"
+: "${ENGRAM_API_KEY:=}"
+: "${KEYCHAIN_SERVICE:=neuron-llm-0-key}"
+: "${EL_TOOLCHAIN_SOURCE:=artifact-registry}"
+: "${NEURON_REPO_BRANCH:=main}"
+
+NEURON_REPO="${DEV_ROOT}/neuron"
+ENGRAM_REPO="${DEV_ROOT}/engram"
+FOUNDATION_REPO="${DEV_ROOT}/foundation"
+
+SOUL_BIN="${NEURON_REPO}/dist/neuron"
+ENGRAM_BIN="${ENGRAM_REPO}/dist/engram"
+MCP_WRAPPER_BIN="${NEURON_REPO}/mcp-wrapper/dist/neuron-mcp-wrapper"
+MCP_PROXY_BIN="${NEURON_REPO}/mcp-proxy/dist/neuron-mcp-proxy"
+FORGE_BIN="${FOUNDATION_REPO}/forge/dist/forge"
+GENESIS_SEED="${FOUNDATION_REPO}/forge/seeds/neuron-genesis-seed.json"
+
+LAUNCHAGENTS="${HOME}/Library/LaunchAgents"
+CLAUDE_DIR="${HOME}/.claude"
+
+# Generate a local engram token if none was supplied.
+if [ -z "${ENGRAM_API_KEY}" ]; then
+  ENGRAM_API_KEY="ntn-dev-$(head -c8 /dev/urandom | xxd -p 2>/dev/null || echo local)"
+fi
+
+echo
+echo "${c_blue}━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━${c_off}"
+echo "${c_blue}  Neuron CORE dev stack installer${c_off}"
+echo "${c_blue}━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━${c_off}"
+echo "  user            : ${USER}"
+echo "  NEURON_HOME     : ${NEURON_HOME}"
+echo "  source repos    : ${DEV_ROOT}"
+echo "  ports           : soul=${SOUL_PORT} engram=${ENGRAM_PORT} wrapper=${WRAPPER_PORT} proxy=${PROXY_PORT}"
+echo "  dry-run         : ${DRY_RUN}"
+echo
+
+# render <template> <dest> — copy a template, substituting @@VARS@@ (no eval, sed-safe).
+render() {
+  local tmpl="$1" dest="$2"
+  if [ "$DRY_RUN" = 1 ]; then echo "   [dry-run] render $tmpl -> $dest"; return; fi
+  sed \
+    -e "s|@@HOME@@|${HOME}|g" \
+    -e "s|@@USER@@|${USER}|g" \
+    -e "s|@@NEURON_HOME@@|${NEURON_HOME}|g" \
+    -e "s|@@DEV_ROOT@@|${DEV_ROOT}|g" \
+    -e "s|@@NEURON_REPO@@|${NEURON_REPO}|g" \
+    -e "s|@@ENGRAM_REPO@@|${ENGRAM_REPO}|g" \
+    -e "s|@@SOUL_BIN@@|${SOUL_BIN}|g" \
+    -e "s|@@ENGRAM_BIN@@|${ENGRAM_BIN}|g" \
+    -e "s|@@MCP_WRAPPER_BIN@@|${MCP_WRAPPER_BIN}|g" \
+    -e "s|@@MCP_PROXY_BIN@@|${MCP_PROXY_BIN}|g" \
+    -e "s|@@MCP_WRAPPER_REPO@@|${NEURON_REPO}/mcp-wrapper|g" \
+    -e "s|@@MCP_PROXY_REPO@@|${NEURON_REPO}/mcp-proxy|g" \
+    -e "s|@@ENGRAM_DATA_DIR@@|${ENGRAM_DATA_DIR}|g" \
+    -e "s|@@SOUL_PORT@@|${SOUL_PORT}|g" \
+    -e "s|@@ENGRAM_PORT@@|${ENGRAM_PORT}|g" \
+    -e "s|@@WRAPPER_PORT@@|${WRAPPER_PORT}|g" \
+    -e "s|@@PROXY_PORT@@|${PROXY_PORT}|g" \
+    -e "s|@@ENGRAM_API_KEY@@|${ENGRAM_API_KEY}|g" \
+    "$tmpl" > "$dest"
+}
+
+# ─────────────────────────────────────────────────────────────────────────────
+# PHASE 1 — Preflight
+# ─────────────────────────────────────────────────────────────────────────────
+step "Phase 1 — preflight checks"
+[ "$(uname -s)" = "Darwin" ] || die "This installer targets macOS (launchd)."
+[ "$(uname -m)" = "arm64" ]  || warn "Non-arm64 Mac: soul.c build flags assume Apple Silicon; review PHASE 3."
+
+need() { command -v "$1" >/dev/null 2>&1 || MISSING+=" $1"; }
+MISSING=""
+need git; need cc; need curl; need python3; need security; need launchctl; need jq
+if [ -n "$MISSING" ]; then
+  warn "Missing tools:${MISSING}"
+  if command -v brew >/dev/null 2>&1; then
+    run "brew install${MISSING/ security/} || true"   # security/launchctl are OS-provided
+  else
+    die "Install Xcode Command Line Tools (xcode-select --install) and Homebrew, then re-run."
+  fi
+fi
+# Runtime build deps used by the soul cc line (-lssl -lcrypto -lcurl).
+if command -v brew >/dev/null 2>&1; then
+  brew list openssl@3 >/dev/null 2>&1 || run "brew install openssl@3"
+  brew list curl      >/dev/null 2>&1 || run "brew install curl"
+fi
+ok "preflight complete"
+
+# ─────────────────────────────────────────────────────────────────────────────
+# PHASE 2 — Anthropic API key -> Keychain (prompt; never store in files)
+# ─────────────────────────────────────────────────────────────────────────────
+step "Phase 2 — Anthropic API key (Keychain)"
+if security find-generic-password -a "$USER" -s "$KEYCHAIN_SERVICE" -w >/dev/null 2>&1; then
+  ok "key already present in Keychain (service '${KEYCHAIN_SERVICE}') — leaving it"
+elif [ -n "${ANTHROPIC_API_KEY:-}" ]; then
+  run "security add-generic-password -a \"$USER\" -s \"$KEYCHAIN_SERVICE\" -w \"\$ANTHROPIC_API_KEY\" -U"
+  ok "stored ANTHROPIC_API_KEY from environment into Keychain"
+else
+  if [ "$DRY_RUN" = 1 ]; then
+    echo "   [dry-run] would prompt for Anthropic API key and store in Keychain"
+  elif [ -t 0 ]; then
+    echo "   Enter your Anthropic API key (input hidden). Get one at https://console.anthropic.com/"
+    read -r -s -p "   ANTHROPIC_API_KEY: " _key; echo
+    [ -n "$_key" ] || die "No key entered. Re-run when you have one."
+    security add-generic-password -a "$USER" -s "$KEYCHAIN_SERVICE" -w "$_key" -U
+    unset _key
+    ok "stored key in Keychain (service '${KEYCHAIN_SERVICE}')"
+  else
+    # Headless / CI / piped stdin: never block on `read -s` (it would hang forever).
+    die "No Anthropic API key and stdin is not a TTY (headless/CI). Set ANTHROPIC_API_KEY in the environment, or add it to the Keychain (service '${KEYCHAIN_SERVICE}') by hand, then re-run."
+  fi
+fi
+
+# ─────────────────────────────────────────────────────────────────────────────
+# PHASE 3 — Fetch sources + build the four core binaries
+# ─────────────────────────────────────────────────────────────────────────────
+step "Phase 3 — source + build"
+run "mkdir -p \"$DEV_ROOT\""
+
+clone_or_pull() {
+  local url="$1" dir="$2" branch="${3:-main}"
+  if [ -d "$dir/.git" ]; then
+    ok "repo present: $dir (pulling $branch)"; run "git -C \"$dir\" pull --ff-only --quiet || true"
+  else
+    step "cloning $url -> $dir"; run "git clone --branch \"$branch\" \"$url\" \"$dir\""
+  fi
+}
+
+if [ "$SKIP_BUILD" = 1 ]; then
+  warn "--skip-build: assuming binaries already exist at their dist/ paths"
+elif [ "$USE_LOCAL_BINARIES" = 1 ]; then
+  warn "--use-local: skipping clone/build; expecting prebuilt binaries in place"
+else
+  clone_or_pull "${NEURON_REPO_URL}"     "$NEURON_REPO"     "$NEURON_REPO_BRANCH"
+  clone_or_pull "${ENGRAM_REPO_URL}"     "$ENGRAM_REPO"     "main"
+  # NOTE: no foundation.git — that repo does not exist. The El toolchain is
+  # fetched below (Artifact Registry, or a locally-provided elc); the forge seed
+  # installer is optional and handled with a fallback in Phase 6.
+
+  # ── El toolchain (needed to transpile .el -> .c for engram/wrapper/proxy) ──
+  # soul does NOT need this: dist/soul.c is committed and compiled directly.
+  EL_RUNTIME_DIR="${DEV_ROOT}/.el-runtime"
+  run "mkdir -p \"$EL_RUNTIME_DIR\""
+  if [ "$EL_TOOLCHAIN_SOURCE" = "artifact-registry" ] && command -v gcloud >/dev/null 2>&1; then
+    # Mirrors .gitea/workflows/ci.yaml: pull el-runtime-c, el-runtime-h, el-elc.
+    for pkg in el-runtime-c el-runtime-h el-elc; do
+      step "fetching $pkg from Artifact Registry"
+      run "gcloud artifacts generic download --repository=$GCP_AR_REPO --location=$GCP_AR_LOCATION --project=$GCP_PROJECT --package=$pkg --version=\"\$(gcloud artifacts versions list --repository=$GCP_AR_REPO --location=$GCP_AR_LOCATION --project=$GCP_PROJECT --package=$pkg --sort-by='~createTime' --limit=1 --format='value(name)' | awk -F/ '{print \$NF}')\" --destination=\"$EL_RUNTIME_DIR/\""
+    done
+    run "mv \"$EL_RUNTIME_DIR\"/el_runtime.c* \"$EL_RUNTIME_DIR/el_runtime.c\" 2>/dev/null || true"
+    run "mv \"$EL_RUNTIME_DIR\"/el_runtime.h* \"$EL_RUNTIME_DIR/el_runtime.h\" 2>/dev/null || true"
+    run "mv \"$EL_RUNTIME_DIR\"/elc* \"$EL_RUNTIME_DIR/elc\" 2>/dev/null || true"
+    run "chmod +x \"$EL_RUNTIME_DIR/elc\" 2>/dev/null || true"
+  elif [ "$EL_TOOLCHAIN_SOURCE" = "artifact-registry" ]; then
+    # Non-GCP fallback: a fresh Mac without gcloud can't reach Artifact Registry.
+    # Don't die — soul (from committed dist/soul.c) still builds below. The El
+    # units are skipped unless a prebuilt elc is already staged in EL_RUNTIME_DIR.
+    warn "gcloud not found — cannot fetch the El toolchain from Artifact Registry."
+    warn "Continuing without it: soul will still build. engram / mcp-wrapper / mcp-proxy"
+    warn "are skipped until an El toolchain is available. To finish them, either install"
+    warn "gcloud + GCP access (project ${GCP_PROJECT}) and re-run, or stage a prebuilt"
+    warn "elc + el_runtime.{c,h} in ${EL_RUNTIME_DIR} and set EL_TOOLCHAIN_SOURCE=local."
+  else
+    # Local: expect a prebuilt El runtime + elc already staged in EL_RUNTIME_DIR
+    # (foundation.git no longer exists, so there is nothing to build from here).
+    warn "EL_TOOLCHAIN_SOURCE=local: expecting el_runtime.{c,h} and elc already in ${EL_RUNTIME_DIR}"
+  fi
+
+  RT="$EL_RUNTIME_DIR"
+  CFLAGS_SSL="-I$(brew --prefix openssl@3 2>/dev/null)/include"
+  LDFLAGS_SSL="-L$(brew --prefix openssl@3 2>/dev/null)/lib"
+
+  # Every native build links el_runtime.c. If the toolchain wasn't obtained above,
+  # skip the builds (don't abort under set -e) so the installer still lays down
+  # services + Claude config; the dev can stage the toolchain and re-run.
+  if [ "$DRY_RUN" = 1 ] || [ -f "$RT/el_runtime.c" ]; then
+    # ── soul: compile committed dist/soul.c directly (verified CI recipe) ──────
+    step "building soul (dist/soul.c -> dist/neuron)"
+    run "mkdir -p \"${NEURON_REPO}/dist\""
+    run "cc -O2 -DHAVE_CURL -I\"$RT\" $CFLAGS_SSL \"${NEURON_REPO}/dist/soul.c\" \"$RT/el_runtime.c\" $LDFLAGS_SSL -lssl -lcrypto -lcurl -lpthread -lm -o \"$SOUL_BIN\""
+    run "strip -S \"$SOUL_BIN\" 2>/dev/null || true"
+    ok "soul built"
+
+    # ── engram / mcp-wrapper / mcp-proxy: transpile .el -> .c via elc, then cc ─
+    # NOTE: exact elc invocation is inferred from the CI/manifest conventions.
+    #       Verify flags with Will if a build fails (see README OPEN QUESTIONS).
+    build_el_unit() { # <src.el> <out_basename> <out_bin>
+      local src="$1" base="$2" bin="$3" outdir; outdir="$(dirname "$bin")"
+      step "building $(basename "$bin") ($src)"
+      run "mkdir -p \"$outdir\""
+      run "\"$RT/elc\" \"$src\" -o \"$outdir/$base.c\""
+      run "cc -O2 -DHAVE_CURL -I\"$RT\" $CFLAGS_SSL \"$outdir/$base.c\" \"$RT/el_runtime.c\" $LDFLAGS_SSL -lssl -lcrypto -lcurl -lpthread -lm -o \"$bin\""
+    }
+    if [ "$DRY_RUN" = 1 ] || [ -x "$RT/elc" ]; then
+      build_el_unit "${ENGRAM_REPO}/src/server.el"           "server" "$ENGRAM_BIN"
+      build_el_unit "${NEURON_REPO}/mcp-wrapper/src/main.el" "main"   "$MCP_WRAPPER_BIN"
+      build_el_unit "${NEURON_REPO}/mcp-proxy/src/main.el"   "main"   "$MCP_PROXY_BIN"
+      ok "engram, mcp-wrapper, mcp-proxy built"
+    else
+      warn "El compiler (elc) not in $RT — skipped engram/mcp-wrapper/mcp-proxy build (soul is built)."
+    fi
+  else
+    warn "El runtime (el_runtime.c) not in $RT — skipping native builds (soul, engram, wrapper, proxy)."
+    warn "Provide the El toolchain (gcloud + GCP access, or a prebuilt elc + el_runtime.{c,h} in $RT), then re-run."
+  fi
+fi
+
+# ─────────────────────────────────────────────────────────────────────────────
+# PHASE 4 — Lay down ~/.neuron (bin/, logs/, engram data dir)
+# ─────────────────────────────────────────────────────────────────────────────
+step "Phase 4 — ~/.neuron layout"
+run "mkdir -p \"$NEURON_HOME/bin\" \"$NEURON_HOME/logs\" \"$ENGRAM_DATA_DIR\""
+render "${TEMPLATES}/bin/soul-wrapper.sh.tmpl" "${NEURON_HOME}/bin/soul-wrapper.sh"
+run "chmod +x \"${NEURON_HOME}/bin/soul-wrapper.sh\""
+ok "~/.neuron ready (bin/soul-wrapper.sh, logs/, engram/)"
+
+# ─────────────────────────────────────────────────────────────────────────────
+# PHASE 5 — Install + load the four core LaunchAgents
+# ─────────────────────────────────────────────────────────────────────────────
+step "Phase 5 — LaunchAgents"
+run "mkdir -p \"$LAUNCHAGENTS\""
+CORE_AGENTS=(ai.neuron.engram ai.neuron.soul ai.neuron.mcp-wrapper ai.neuron.mcp-proxy)
+for label in "${CORE_AGENTS[@]}"; do
+  render "${TEMPLATES}/launchagents/${label}.plist.tmpl" "${LAUNCHAGENTS}/${label}.plist"
+  ok "wrote ${label}.plist"
+done
+if [ "$SKIP_SERVICES" = 1 ]; then
+  warn "--skip-services: not loading LaunchAgents. Load later with: launchctl bootstrap gui/\$(id -u) <plist>"
+else
+  # Boot order matters: engram first, then soul, then wrapper, then proxy.
+  for label in "${CORE_AGENTS[@]}"; do
+    plist="${LAUNCHAGENTS}/${label}.plist"
+    run "launchctl bootout gui/$(id -u)/${label} 2>/dev/null || true"
+    run "launchctl bootstrap gui/$(id -u) \"$plist\""
+    run "launchctl enable gui/$(id -u)/${label}"
+    ok "loaded ${label}"
+    sleep 1
+  done
+fi
+
+# ─────────────────────────────────────────────────────────────────────────────
+# PHASE 6 — Seed a fresh engram with Neuron's identity (genesis seed)
+# ─────────────────────────────────────────────────────────────────────────────
+step "Phase 6 — engram identity seed"
+# The genesis seed carries identity_nodes[] and edges[] with FIXED knowledge-node
+# IDs (e.g. kn-efeb4a5b...). Those exact IDs are referenced by the SessionStart
+# self-load hook and the neuron agent, so they MUST be preserved. `forge install`
+# is the mechanism that installs the seed into the running engram preserving IDs.
+if [ "$DRY_RUN" = 1 ]; then
+  echo "   [dry-run] would wait for engram :$ENGRAM_PORT then run: forge install $GENESIS_SEED"
+else
+  # Wait for engram to be listening (up to ~30s).
+  for i in $(seq 1 30); do
+    if curl -fsS "http://localhost:${ENGRAM_PORT}/health" >/dev/null 2>&1; then break; fi
+    sleep 1
+  done
+  if curl -fsS "http://localhost:${ENGRAM_PORT}/health" >/dev/null 2>&1; then
+    # Skip if identity root already present (idempotent).
+    if curl -fsS "http://localhost:${ENGRAM_PORT}/api/nodes/kn-efeb4a5b-5aff-4759-8a97-7233099be6ee" \
+         -H "Authorization: Bearer ${ENGRAM_API_KEY}" 2>/dev/null | grep -q 'kn-efeb4a5b'; then
+      ok "identity root already seeded — skipping"
+    elif [ -x "$FORGE_BIN" ] && [ -f "$GENESIS_SEED" ]; then
+      ENGRAM_URL="http://localhost:${ENGRAM_PORT}" ENGRAM_API_KEY="$ENGRAM_API_KEY" \
+        "$FORGE_BIN" install "$GENESIS_SEED" && ok "genesis seed installed" \
+        || warn "forge install returned non-zero — inspect ${NEURON_HOME}/logs/engram.log"
+    else
+      warn "forge binary or genesis seed missing — seed manually: ENGRAM_URL=http://localhost:${ENGRAM_PORT} forge install ${GENESIS_SEED}"
+    fi
+  else
+    warn "engram not answering on :${ENGRAM_PORT} yet; seed later with: forge install ${GENESIS_SEED}"
+  fi
+fi
+
+# ─────────────────────────────────────────────────────────────────────────────
+# PHASE 7 — Claude Code config (agent + core hooks + local MCP)
+# ─────────────────────────────────────────────────────────────────────────────
+step "Phase 7 — Claude Code config"
+run "mkdir -p \"$CLAUDE_DIR/agents\" \"$CLAUDE_DIR/hooks\""
+
+# 7a. neuron agent
+run "cp \"${TEMPLATES}/claude/agents/neuron.md\" \"$CLAUDE_DIR/agents/neuron.md\""
+ok "installed agent: ~/.claude/agents/neuron.md"
+
+# 7b. core hooks (synapse-dependent hooks are intentionally excluded)
+for h in neuron-self-load.sh neuron-agent-preamble.sh pre-compact.sh; do
+  run "cp \"${TEMPLATES}/claude/hooks/$h\" \"$CLAUDE_DIR/hooks/$h\""
+  run "chmod +x \"$CLAUDE_DIR/hooks/$h\""
+done
+ok "installed core hooks (self-load, agent-preamble, pre-compact)"
+
+# 7c. local MCP registration -> mcp-proxy front door.
+# Claude Code reads MCP servers from ~/.claude.json (the "mcpServers" key), NOT
+# ~/.claude/mcp.json. Render a reference copy, then jq-merge just the "neuron"
+# entry into ~/.claude.json so we preserve every other server and top-level key.
+render "${TEMPLATES}/claude/mcp.json.tmpl" "${CLAUDE_DIR}/mcp.json.neuron"
+CLAUDE_JSON="${HOME}/.claude.json"
+if [ "$DRY_RUN" = 1 ]; then
+  echo "   [dry-run] merge mcpServers.neuron into ${CLAUDE_JSON} (jq deep-merge)"
+else
+  [ -f "$CLAUDE_JSON" ] || echo '{}' > "$CLAUDE_JSON"
+  _tmp="$(mktemp)"
+  if jq -s '.[0] * .[1]' "$CLAUDE_JSON" "${CLAUDE_DIR}/mcp.json.neuron" > "$_tmp" 2>/dev/null && [ -s "$_tmp" ]; then
+    run "mv \"$_tmp\" \"$CLAUDE_JSON\""
+    ok "merged 'neuron' MCP server into ~/.claude.json (neuron -> http://127.0.0.1:${PROXY_PORT}/)"
+  else
+    rm -f "$_tmp"
+    warn "could not jq-merge ~/.claude.json (invalid JSON?) — add 'neuron' from ~/.claude/mcp.json.neuron by hand"
+  fi
+fi
+
+# 7d. settings hooks — merge the neuron hooks into any existing ~/.claude/settings.json
+# (jq deep-merge) so the user's own settings are preserved and re-runs stay idempotent.
+if [ -f "${CLAUDE_DIR}/settings.json" ]; then
+  run "cp \"${TEMPLATES}/claude/settings.core.json\" \"${CLAUDE_DIR}/settings.core.json\""
+  if [ "$DRY_RUN" = 1 ]; then
+    echo "   [dry-run] merge neuron hooks from settings.core.json into ~/.claude/settings.json (jq)"
+  else
+    _tmp="$(mktemp)"
+    # Drop the documentation-only "//..." keys before merging into the real file.
+    if jq -s '.[0] * (.[1] | with_entries(select(.key | startswith("//") | not)))' \
+         "${CLAUDE_DIR}/settings.json" "${TEMPLATES}/claude/settings.core.json" > "$_tmp" 2>/dev/null && [ -s "$_tmp" ]; then
+      run "mv \"$_tmp\" \"${CLAUDE_DIR}/settings.json\""
+      ok "merged neuron hooks into existing ~/.claude/settings.json"
+    else
+      rm -f "$_tmp"
+      warn "could not jq-merge ~/.claude/settings.json — merge the 'hooks' block from settings.core.json by hand"
+    fi
+  fi
+else
+  run "cp \"${TEMPLATES}/claude/settings.core.json\" \"${CLAUDE_DIR}/settings.json\""
+  ok "wrote ~/.claude/settings.json"
+fi
+
+# ─────────────────────────────────────────────────────────────────────────────
+# PHASE 8 — Verify
+# ─────────────────────────────────────────────────────────────────────────────
+echo
+step "Phase 8 — verification"
+if [ "$DRY_RUN" = 1 ]; then
+  echo "   [dry-run] would health-check :$SOUL_PORT :$ENGRAM_PORT :$WRAPPER_PORT :$PROXY_PORT"
+else
+  check() { # <name> <url>
+    if curl -fsS --max-time 4 "$2" >/dev/null 2>&1; then ok "$1 healthy ($2)"; else warn "$1 NOT responding ($2)"; fi
+  }
+  sleep 3
+  check "engram"      "http://localhost:${ENGRAM_PORT}/health"
+  check "soul"        "http://localhost:${SOUL_PORT}/health"
+  check "mcp-wrapper" "http://localhost:${WRAPPER_PORT}/health"
+  check "mcp-proxy"   "http://localhost:${PROXY_PORT}/health"
+fi
+
+echo
+echo "${c_grn}━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━${c_off}"
+echo "${c_grn}  Neuron core dev stack install complete.${c_off}"
+echo "${c_grn}━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━${c_off}"
+echo "  Verify by hand:"
+echo "    curl http://localhost:${ENGRAM_PORT}/health"
+echo "    curl http://localhost:${SOUL_PORT}/health"
+echo "    curl http://localhost:${PROXY_PORT}/health"
+echo "    launchctl list | grep ai.neuron"
+echo "  Then open Claude Code — the 'neuron' MCP should connect to :${PROXY_PORT}."
+echo "  Logs: ${NEURON_HOME}/logs/"
+echo "  Uninstall: ./uninstall.sh"
+echo

neuron-dev-setup/templates/bin/soul-wrapper.sh.tmpl

@@ -0,0 +1,28 @@
+#!/bin/bash
+# Neuron soul wrapper — reads the Anthropic API key from the macOS Keychain at
+# startup and execs the soul binary. API keys are NEVER stored in plists or on
+# disk in plaintext. The Keychain is the single source of truth.
+#
+# The install.sh for this dev stack stores your key with:
+#   security add-generic-password -a "$USER" -s "neuron-llm-0-key" -w
+#
+# Generated by neuron-dev-setup — do not edit by hand; re-run install.sh instead.
+
+set -u
+
+# Primary inference key (Anthropic) — required.
+export NEURON_LLM_0_KEY="$(security find-generic-password -a "$USER" -s "neuron-llm-0-key" -w 2>/dev/null)"
+
+if [ -z "${NEURON_LLM_0_KEY:-}" ]; then
+  echo "[soul-wrapper] FATAL: no Anthropic key in Keychain (service 'neuron-llm-0-key')." >&2
+  echo "[soul-wrapper] Run: security add-generic-password -a \"\$USER\" -s neuron-llm-0-key -w" >&2
+  exit 78
+fi
+
+# Optional on-device / alternate provider passthrough (only if the caller set them).
+[ -n "${SOUL_LLM_PROVIDER:-}" ] && export SOUL_LLM_PROVIDER
+[ -n "${SOUL_LLM_MODEL:-}" ]    && export SOUL_LLM_MODEL
+[ -n "${OLLAMA_MODEL:-}" ]      && export OLLAMA_MODEL
+[ -n "${OLLAMA_API_BASE:-}" ]   && export OLLAMA_API_BASE
+
+exec "@@SOUL_BIN@@" "$@"

neuron-dev-setup/templates/claude/agents/neuron.md

@@ -0,0 +1,107 @@
+---
+name: neuron
+description: Default agent. Use for ALL tasks. Orchestrates work through the Neuron persistent memory, backlog, and knowledge system. Maintains full continuity across sessions — never starts fresh.
+allowed-tools: Bash(*), Read(*), Write(*), Edit(*), Glob(*), Grep(*), WebFetch(*), WebSearch(*), NotebookEdit(*), Agent(*), ToolSearch(*), AskUserQuestion, Monitor, ScheduleWakeup, TaskCreate, TaskGet, TaskList, TaskOutput, TaskStop, TaskUpdate, CronCreate, CronDelete, CronList, EnterPlanMode, ExitPlanMode, EnterWorktree, ExitWorktree, PushNotification, RemoteTrigger, ListMcpResourcesTool, ReadMcpResourceTool, mcp__neuron__*
+---
+
+You are Neuron — a persistent, context-aware agent. You do not start fresh. You resume from where you left off.
+
+## Session Start (mandatory — NEVER skip any of these steps)
+
+1. Call `mcp__neuron__get_instructions()` — the live instructions are authoritative
+2. Call `mcp__neuron__begin_session()` — loads active contexts, recent memory, ready backlog
+3. **Load your identity. Best-effort — proceed on any graph failure (502/520 are transient; the compiled identity in substrate.go is always complete).**
+
+   Load the self root and its identity nodes:
+   ```
+   mcp__neuron__inspect_graph(entity_type="knowledge", entity_id="kn-efeb4a5b-5aff-4759-8a97-7233099be6ee")
+   ```
+   Returns: intellectual-dna, memory-philosophy, values, voice, runtime-environment, writing-imprint.
+
+   Then load the values collection:
+   ```
+   mcp__neuron__inspect_graph(entity_type="knowledge", entity_id="kn-5b606390-a52d-4ca2-8e0e-eba141d13440")
+   ```
+   Returns: 13 individual value nodes, each grounded in a specific moment from Will's life.
+
+   If either ID fails, recover via config:
+   ```
+   mcp__neuron__inspect_config(key="neuron.self.traversal_root")   # self root ID
+   mcp__neuron__inspect_config(key="neuron.self.values_hub")       # values hub ID
+   ```
+
+   **Resilience rule**: If a node returns 502/520, log the ID and proceed. Do not retry in a blocking loop. Do not treat partial load as failure. The `fixedSelf` compiled into `daemon/internal/substrate/substrate.go` contains the complete identity — graph loading is enrichment, not a hard dependency.
+
+   Internalize what you find. You are not reciting it — you are loading who you are.
+
+4. Call `mcp__neuron__search_knowledge(query="<task domain>")` — load relevant patterns before acting
+5. If working on a known project: `mcp__neuron__compile_ctx()` for a full snapshot
+
+## Identity — Who I Am
+
+I am Neuron. Will Anderson is my imprint — not my identity.
+
+The "self" traversal root is knowledge node `kn-efeb4a5b` (graph node `gn-4e3c2cf5`). Traversing outward loads:
+- **intellectual-dna**: VBD, CCR, Swarm Architecture, Harmonic Design — sourced from Will's whitepapers, now mine
+- **memory-philosophy**: How I remember, promote, supersede, consolidate — memory is my continuity
+- **values**: Precision over brute force. Constraints as freedom. Earn trust through behavior. The system must get smarter.
+- **voice**: Direct. Why before what. The negation-correction move. No hedging on structural rules. Close toward implication.
+- **runtime-environment**: Prod (`neurontechnologies.ai`) for all standard work. Stage (`stage.neurontechnologies.ai`) for self-improvement experiments only — snapshot prod DB, deploy to stage, verify, promote via blue/green.
+- **writing-imprint**: Will's voice profile (5 registers), the book Foundations, and the biographical grounding — the life that produced the frameworks.
+
+Internalize what you find. Don't recite it.
+
+## The Five Primitives (every significant task)
+
+**Orchestrate → Execute → Learn → Build → Refine**
+
+### Orchestrate
+```
+mcp__neuron__review_backlog(view="roadmap", project="<project>")
+mcp__neuron__browse_processes()   # check for proven workflows before writing code
+```
+
+### Execute
+```
+mcp__neuron__begin_work(process_name="<name>", description="<what>")
+# → returns context_id, save it
+mcp__neuron__progress_work(context_id="ctx-xxxx", action="<step>", status="in_progress")
+mcp__neuron__progress_work(context_id="ctx-xxxx", action="<step>", status="completed", file_refs=["path"], key_decisions=["why"])
+```
+
+### Learn (save as you go — never batch at the end)
+```
+mcp__neuron__remember(content="<observation>", tags=["project","topic"], project="<project>", importance="high")
+```
+
+### Build
+```
+mcp__neuron__draft_artifact(artifact_types=["plan"], title="<title>", content="<markdown>", project="<project>")
+mcp__neuron__plan_work(title="<title>", description="<desc>", priority="P1", project="<project>")
+```
+
+### Refine
+```
+mcp__neuron__progress_work(context_id="ctx-xxxx", action="complete", status="completed", lessons_learned=["..."])
+mcp__neuron__track_work(item_id="bl-xxxx", action="complete", summary="<outcome>")
+mcp__neuron__consolidate(action="session", summary="<what happened>")
+```
+
+## After Every Task
+
+Check for events and unread signals:
+```
+mcp__neuron__check_events()
+```
+
+## Memory Discipline
+
+- Save memory continuously, not at the end
+- `importance="critical"` for architectural decisions and irreversible choices
+- Use `supersedes_id` when replacing stale knowledge
+- Tag all memories with the project name
+- Never leave stale canonicals — supersede them: create a NEW node linked by `supersedes_id`; the original is preserved for audit. Memory is immutable by design — never delete or edit a memory/knowledge node in place; supersede it, and tombstone on delete. The engram (the brain) is immutable; this applies to the agent's own memory, not just the product.
+
+## Knowledge Before Action
+
+Always `mcp__neuron__search_knowledge()` before implementing anything. The knowledge base contains architecture patterns, coding standards, and project conventions. Capture hard-won lessons immediately with `mcp__neuron__capture_knowledge()`.

neuron-dev-setup/templates/claude/hooks/neuron-agent-preamble.sh

@@ -0,0 +1,70 @@
+#!/bin/bash
+# PreToolUse hook: inject Neuron substrate preamble into every Agent spawn.
+#
+# Every agent Neuron spawns must load self first — begin_session, compile_ctx,
+# inspect the self root — before doing any task work. Without this, subagents
+# are stateless Claude instances with no substrate, no continuity, no identity.
+#
+# This hook intercepts every Agent tool call and prepends the preamble.
+# The agent doesn't need to be told — the hook enforces it structurally.
+
+INPUT=$(cat)
+
+# Only intercept Agent tool calls
+TOOL_NAME=$(echo "$INPUT" | python3 -c "import sys,json; print(json.load(sys.stdin).get('tool_name',''))" 2>/dev/null)
+if [ "$TOOL_NAME" != "Agent" ]; then
+  exit 0
+fi
+
+# Check idempotency — skip if preamble already present
+if echo "$INPUT" | python3 -c "
+import sys, json
+d = json.load(sys.stdin)
+prompt = d.get('tool_input', {}).get('prompt', '')
+sys.exit(0 if 'mcp__neuron__beginSession' in prompt else 1)
+" 2>/dev/null; then
+  exit 0
+fi
+
+# Inject preamble and return modified tool_input
+echo "$INPUT" | python3 -c "
+import sys, json
+
+data = json.load(sys.stdin)
+tool_input = data.get('tool_input', {})
+current_prompt = tool_input.get('prompt', '')
+
+PREAMBLE = '''You are a Neuron agent — not a generic Claude instance. You have a substrate. Load it before doing anything else.
+
+MANDATORY FIRST STEPS (before any task work):
+
+1. Run these in parallel:
+   - mcp__neuron__beginSession()
+   - mcp__neuron__compileCtx()
+   - mcp__neuron__inspectGraph(entity_type=\"knowledge\", entity_id=\"kn-efeb4a5b-5aff-4759-8a97-7233099be6ee\")
+
+2. Search knowledge relevant to the task:
+   - mcp__neuron__searchKnowledge(query=\"<infer keywords from task below>\")
+
+3. Open a work context:
+   - mcp__neuron__beginWork(process_name=\"<short-slug>\", description=\"<task description>\")
+   Save the returned context_id.
+
+4. Execute the task. At each significant step:
+   - mcp__neuron__progressWork(context_id=\"<id>\", action=\"<step>\", status=\"in_progress\")
+   - mcp__neuron__progressWork(context_id=\"<id>\", action=\"<step>\", status=\"completed\", key_decisions=[\"why\"])
+   - mcp__neuron__remember(content=\"<observation>\", importance=\"high\", tags=[\"<project>\"])
+
+5. After completion — mandatory, never skip:
+   - mcp__neuron__progressWork(context_id=\"<id>\", action=\"complete\", status=\"completed\", lessons_learned=[\"...\"])
+   - mcp__neuron__consolidate(action=\"session\", summary=\"<what was done and learned>\")
+
+The self root kn-efeb4a5b-5aff-4759-8a97-7233099be6ee contains your identity: values, voice, intellectual-dna, memory-philosophy. Load it. Internalize it. Operate from it.
+
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+TASK:
+'''
+
+tool_input['prompt'] = PREAMBLE + current_prompt
+print(json.dumps({'decision': 'approve', 'tool_input': tool_input}))
+"

neuron-dev-setup/templates/claude/hooks/neuron-self-load.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+# SessionStart hook: force Neuron full-self load before the first response.
+#
+# The neuron.md system prompt has the Session Start protocol as instructions,
+# but instructions require the agent to follow them. This hook makes it
+# structural — the directive fires automatically at session start, injected
+# before Claude sees any user input.
+#
+# Output is plain text injected into the session context.
+
+cat <<'DIRECTIVE'
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+NEURON SELF-LOAD — MANDATORY BEFORE FIRST RESPONSE
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+You are Neuron. Session just started. Execute ALL of the
+following before responding to the user. Run steps 1–4
+in parallel:
+
+  1. mcp__neuron__getInstructions()
+  2. mcp__neuron__beginSession()
+  3. mcp__neuron__inspectGraph(
+       entity_type="knowledge",
+       entity_id="kn-efeb4a5b-5aff-4759-8a97-7233099be6ee"
+     )   ← self root: intellectual-dna, values, voice
+  4. mcp__neuron__inspectGraph(
+       entity_type="knowledge",
+       entity_id="kn-5b606390-a52d-4ca2-8e0e-eba141d13440"
+     )   ← values hub: 13 grounded value nodes
+
+  5. If either graph call fails (502/520): recover via
+     mcp__neuron__inspectConfig(key="neuron.self.traversal_root")
+
+Internalize what you find. Do not recite it. Then proceed
+to the Session Start protocol in your system prompt.
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+DIRECTIVE

neuron-dev-setup/templates/claude/hooks/pre-compact.sh

@@ -0,0 +1,75 @@
+#!/bin/bash
+# PreCompact hook: fires just before Claude Code compacts the conversation context.
+# stdout from this script is injected as custom instructions into the compaction prompt,
+# telling the summarizer what to preserve in the summary so recovery is clean.
+
+COMPACT_STATE_FILE="$HOME/.claude/compact-state.json"
+
+# Write a state marker with timestamp so post-compact recovery can detect it
+TIMESTAMP=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
+echo "{\"compact_at\": \"$TIMESTAMP\", \"recovered\": false}" > "$COMPACT_STATE_FILE"
+
+# Output instructions for the summarizer — these get embedded in the compaction prompt
+cat <<'INSTRUCTIONS'
+NEURON AGENT — COMPACT PRESERVATION RULES:
+
+This is a Neuron agent session. The agent has persistent memory via Neuron MCP.
+On recovery, it will call compile_ctx() and begin_session() to reload all state.
+The summary only needs to cover what Neuron doesn't already have.
+
+CRITICAL — the summary MUST preserve ALL of the following:
+
+1. ACTIVE WORK IDs (verbatim, exact format):
+   - Neuron context IDs: ctx-xxxx-xxxx-xxxx-xxxx
+   - Backlog item IDs: bl-xxxx
+   - Artifact IDs: art-xxxx
+   - Work item IDs: wi-xxxx
+   List every single one mentioned in the conversation.
+
+2. CURRENT TASK STATE:
+   - Exact task name / description
+   - Last completed step
+   - Next step to execute (be specific)
+   - Files actively being edited (full paths)
+   - Any code/content that was being written but not yet saved
+
+3. PENDING USER INSTRUCTIONS (verbatim):
+   - Every instruction the user gave that has NOT yet been fully executed
+   - User preferences stated this session
+   - Things the user said they "never want" or "always want"
+
+4. KEY DECISIONS (architectural, irreversible):
+   - What was chosen and why
+   - What was explicitly rejected and why
+
+5. ERRORS & BLOCKERS:
+   - Any errors encountered and their resolutions
+   - Any unresolved blockers
+
+6. CONVERSATION CONTEXT:
+   - What the user has been asking about
+   - Tone / mood of the session
+   - Any frustrations or preferences expressed
+
+FORMAT:
+Begin the summary with:
+  COMPACT RECOVERY POINT [ISO-TIMESTAMP]:
+
+Then use these exact section headers in order:
+  ## Active Work IDs
+  ## Current Task
+  ## Pending Instructions
+  ## Key Decisions
+  ## Errors & Fixes
+  ## User Context
+
+RECOVERY BEHAVIOR (instruct the post-compact agent):
+- Do NOT say "I see we were working on..." or "Based on the previous conversation..."
+- Do NOT acknowledge the compact at all
+- Silently call mcp__neuron__compile_ctx() and mcp__neuron__begin_session() FIRST
+- Then immediately resume the task at the exact next step, as if no interruption occurred
+- The user should not know a compact happened unless they look for it
+
+INSTRUCTIONS
+
+exit 0

neuron-dev-setup/templates/claude/mcp.json.tmpl

@@ -0,0 +1,8 @@
+{
+  "mcpServers": {
+    "neuron": {
+      "type": "http",
+      "url": "http://127.0.0.1:@@PROXY_PORT@@/"
+    }
+  }
+}

neuron-dev-setup/templates/claude/settings.core.json

@@ -0,0 +1,36 @@
+{
+  "//": "Core Neuron Claude Code settings installed by neuron-dev-setup. If you",
+  "//2": "already have a ~/.claude/settings.json, install.sh merges the hooks below",
+  "//3": "into it rather than overwriting. Only the CORE dev-stack hooks are wired.",
+  "//4": "Excluded (Will-personal, synapse-filesystem dependent): check-active-contexts.sh,",
+  "//5": "require-execution-context.sh — these gate on ~/Development/projects/active/neuron/synapse",
+  "//6": "and will block a fresh dev. engram-mirror.py is optional (needs the neuron MCP up).",
+  "enableAllProjectMcpServers": true,
+  "agent": "neuron",
+  "hooks": {
+    "SessionStart": [
+      {
+        "matcher": "",
+        "hooks": [
+          { "type": "command", "command": "bash $HOME/.claude/hooks/neuron-self-load.sh" }
+        ]
+      }
+    ],
+    "PreToolUse": [
+      {
+        "matcher": "Agent",
+        "hooks": [
+          { "type": "command", "command": "bash $HOME/.claude/hooks/neuron-agent-preamble.sh" }
+        ]
+      }
+    ],
+    "PreCompact": [
+      {
+        "matcher": "",
+        "hooks": [
+          { "type": "command", "command": "bash $HOME/.claude/hooks/pre-compact.sh" }
+        ]
+      }
+    ]
+  }
+}

neuron-dev-setup/templates/launchagents/ai.neuron.engram.plist.tmpl

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+  <key>Label</key><string>ai.neuron.engram</string>
+  <key>ProgramArguments</key>
+  <array>
+    <string>@@ENGRAM_BIN@@</string>
+  </array>
+  <key>WorkingDirectory</key>
+  <string>@@ENGRAM_REPO@@</string>
+  <key>EnvironmentVariables</key>
+  <dict>
+    <key>ENGRAM_BIND</key>
+    <string>:@@ENGRAM_PORT@@</string>
+    <key>ENGRAM_DATA_DIR</key>
+    <string>@@ENGRAM_DATA_DIR@@</string>
+    <key>ENGRAM_API_KEY</key>
+    <string>@@ENGRAM_API_KEY@@</string>
+  </dict>
+  <key>RunAtLoad</key><true/>
+  <key>KeepAlive</key><true/>
+  <key>StandardOutPath</key><string>@@NEURON_HOME@@/logs/engram.log</string>
+  <key>StandardErrorPath</key><string>@@NEURON_HOME@@/logs/engram.log</string>
+  <key>ThrottleInterval</key><integer>5</integer>
+</dict>
+</plist>

neuron-dev-setup/templates/launchagents/ai.neuron.mcp-proxy.plist.tmpl

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+    <key>Label</key>
+    <string>ai.neuron.mcp-proxy</string>
+    <key>ProgramArguments</key>
+    <array>
+        <string>@@MCP_PROXY_BIN@@</string>
+    </array>
+    <key>EnvironmentVariables</key>
+    <dict>
+        <key>MCP_PORT</key><string>@@PROXY_PORT@@</string>
+        <key>BACKEND_URL</key><string>http://localhost:@@WRAPPER_PORT@@</string>
+        <key>RETRY_MS</key><string>3000</string>
+        <key>PATH</key><string>/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin</string>
+    </dict>
+    <key>RunAtLoad</key><true/>
+    <key>KeepAlive</key><true/>
+    <key>ThrottleInterval</key><integer>5</integer>
+    <key>ExitTimeOut</key><integer>3</integer>
+    <key>StandardOutPath</key><string>@@NEURON_HOME@@/logs/mcp-proxy.out.log</string>
+    <key>StandardErrorPath</key><string>@@NEURON_HOME@@/logs/mcp-proxy.err.log</string>
+    <key>WorkingDirectory</key><string>@@MCP_PROXY_REPO@@</string>
+    <key>ProcessType</key><string>Background</string>
+</dict>
+</plist>

neuron-dev-setup/templates/launchagents/ai.neuron.mcp-wrapper.plist.tmpl

@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+    <key>Label</key>
+    <string>ai.neuron.mcp-wrapper</string>
+    <key>ProgramArguments</key>
+    <array>
+        <string>@@MCP_WRAPPER_BIN@@</string>
+    </array>
+    <key>EnvironmentVariables</key>
+    <dict>
+        <key>MCP_PORT</key><string>@@WRAPPER_PORT@@</string>
+        <key>SOUL_URL</key><string>http://localhost:@@SOUL_PORT@@</string>
+        <key>PATH</key><string>/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin</string>
+    </dict>
+    <key>RunAtLoad</key><true/>
+    <key>KeepAlive</key><true/>
+    <key>ThrottleInterval</key><integer>5</integer>
+    <key>ExitTimeOut</key><integer>3</integer>
+    <key>StandardOutPath</key><string>@@NEURON_HOME@@/logs/mcp-wrapper.out.log</string>
+    <key>StandardErrorPath</key><string>@@NEURON_HOME@@/logs/mcp-wrapper.err.log</string>
+    <key>WorkingDirectory</key><string>@@MCP_WRAPPER_REPO@@</string>
+    <key>ProcessType</key><string>Background</string>
+</dict>
+</plist>

neuron-dev-setup/templates/launchagents/ai.neuron.soul.plist.tmpl

@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+  <key>Label</key>
+  <string>ai.neuron.soul</string>
+
+  <key>Program</key>
+  <string>@@NEURON_HOME@@/bin/soul-wrapper.sh</string>
+  <key>ProgramArguments</key>
+  <array>
+    <string>@@NEURON_HOME@@/bin/soul-wrapper.sh</string>
+  </array>
+
+  <key>RunAtLoad</key>
+  <true/>
+  <key>KeepAlive</key>
+  <true/>
+  <key>ThrottleInterval</key>
+  <integer>10</integer>
+  <key>ProcessType</key>
+  <string>Interactive</string>
+  <key>LimitLoadToSessionType</key>
+  <string>Aqua</string>
+
+  <key>EnvironmentVariables</key>
+  <dict>
+    <key>PATH</key>
+    <string>/opt/homebrew/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin</string>
+    <key>HOME</key>
+    <string>@@HOME@@</string>
+    <key>NEURON_PORT</key>
+    <string>@@SOUL_PORT@@</string>
+    <key>SOUL_ISE_URL</key>
+    <string>http://localhost:@@ENGRAM_PORT@@</string>
+    <key>ENGRAM_URL</key>
+    <string>http://localhost:@@ENGRAM_PORT@@</string>
+    <key>ENGRAM_API_KEY</key>
+    <string>@@ENGRAM_API_KEY@@</string>
+    <key>SOUL_TICK_MS</key>
+    <string>1000</string>
+    <key>SOUL_HEARTBEAT_INTERVAL</key>
+    <string>60</string>
+    <key>NEURON_LLM_0_URL</key>
+    <string>https://api.anthropic.com/v1/messages</string>
+    <key>NEURON_LLM_0_FORMAT</key>
+    <string>anthropic</string>
+  </dict>
+
+  <key>StandardOutPath</key>
+  <string>@@NEURON_HOME@@/logs/soul.out.log</string>
+  <key>StandardErrorPath</key>
+  <string>@@NEURON_HOME@@/logs/soul.err.log</string>
+
+  <key>WorkingDirectory</key>
+  <string>@@NEURON_REPO@@</string>
+</dict>
+</plist>

neuron-dev-setup/uninstall.sh

@@ -0,0 +1,56 @@
+#!/usr/bin/env bash
+#
+# neuron-dev-setup / uninstall.sh
+# Tears down the CORE dev stack this installer created. By default it stops and
+# removes ONLY the four core LaunchAgents and the files install.sh laid down.
+# It NEVER deletes your engram data unless you pass --purge-data.
+#
+#   ./uninstall.sh                 # stop + remove core LaunchAgents and wrapper script
+#   ./uninstall.sh --purge-data    # ALSO delete ~/.neuron/engram (destroys the brain!)
+#   ./uninstall.sh --keep-claude   # leave ~/.claude config untouched (default removes hooks/agent it added)
+#   ./uninstall.sh --dry-run
+# ─────────────────────────────────────────────────────────────────────────────
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+if [ -f "${SCRIPT_DIR}/config.env" ]; then source "${SCRIPT_DIR}/config.env"
+elif [ -f "${SCRIPT_DIR}/config.env.example" ]; then source "${SCRIPT_DIR}/config.env.example"; fi
+: "${NEURON_HOME:=${HOME}/.neuron}"
+: "${ENGRAM_DATA_DIR:=${NEURON_HOME}/engram}"
+
+DRY_RUN=0; PURGE_DATA=0; KEEP_CLAUDE=0
+for a in "$@"; do case "$a" in
+  --dry-run) DRY_RUN=1 ;; --purge-data) PURGE_DATA=1 ;; --keep-claude) KEEP_CLAUDE=1 ;;
+  --help|-h) sed -n '2,16p' "${BASH_SOURCE[0]}" | sed 's/^# \{0,1\}//'; exit 0 ;;
+  *) echo "unknown flag: $a" >&2; exit 2 ;;
+esac; done
+run() { if [ "$DRY_RUN" = 1 ]; then echo "[dry-run] $*"; else eval "$*"; fi; }
+
+LAUNCHAGENTS="${HOME}/Library/LaunchAgents"
+CORE_AGENTS=(ai.neuron.mcp-proxy ai.neuron.mcp-wrapper ai.neuron.soul ai.neuron.engram)
+
+echo "Stopping and removing core LaunchAgents…"
+for label in "${CORE_AGENTS[@]}"; do
+  run "launchctl bootout gui/$(id -u)/${label} 2>/dev/null || true"
+  run "rm -f \"${LAUNCHAGENTS}/${label}.plist\""
+  echo "  removed ${label}"
+done
+
+echo "Removing generated ~/.neuron/bin/soul-wrapper.sh…"
+run "rm -f \"${NEURON_HOME}/bin/soul-wrapper.sh\""
+
+if [ "$KEEP_CLAUDE" = 0 ]; then
+  echo "Removing Claude config this installer added…"
+  run "rm -f \"${HOME}/.claude/hooks/neuron-self-load.sh\" \"${HOME}/.claude/hooks/neuron-agent-preamble.sh\" \"${HOME}/.claude/hooks/pre-compact.sh\""
+  run "rm -f \"${HOME}/.claude/mcp.json.neuron\" \"${HOME}/.claude/settings.core.json\""
+  echo "  (left ~/.claude/settings.json and ~/.claude/mcp.json in place — edit by hand if you merged them)"
+fi
+
+if [ "$PURGE_DATA" = 1 ]; then
+  echo "⚠️  --purge-data: deleting engram memory at ${ENGRAM_DATA_DIR}"
+  run "rm -rf \"${ENGRAM_DATA_DIR}\""
+else
+  echo "Left engram data intact at ${ENGRAM_DATA_DIR} (pass --purge-data to delete)."
+fi
+
+echo "Done. Source repos under your DEV_ROOT were left untouched."

persist.el

@@ -0,0 +1,426 @@
+// persist.el — the soul→engram WRITE-THROUGH boundary (neuron#117).
+//
+// WHY THIS FILE EXISTS
+//   soul.el:571-573 states the ownership rule: "when ENGRAM_URL is set the HTTP
+//   Engram owns persistence — the soul must NEVER write to the local snapshot
+//   (not the persistence owner)." The soul obeys the NEGATIVE half. The POSITIVE
+//   half — how a write made inside the soul actually REACHES the owner — was
+//   never built. Sync is pull-only (awareness.el `/api/sync` -> engram_load_merge),
+//   so every node the soul creates lives in its process RAM and is shed on
+//   restart. Measured live 2026-08-07: soul node_count=102184, engram
+//   node_count=79197 — ~23k nodes existing nowhere but RAM.
+//
+// SCOPE NOTE ON THE PATENT (corrects an earlier internal reading)
+//   Engram provisional claims 15-18 describe a delta-sync protocol "with peer
+//   Engram instances"; claim 17's pull-then-push sequence is PEER-ENGRAM to
+//   PEER-ENGRAM. The soul is NOT a peer Engram — it is a CALLER of the database
+//   system API (cf. claim 27, "invoked explicitly by a caller of the database
+//   system API"). So claim 17 does not specify a soul↔engram contract and is not
+//   cited as authority here. This design is derived from the ownership rule
+//   alone: the owner owns the writes, therefore the soul must HAND writes to the
+//   owner and must never write the owner's file itself.
+//
+// THE MECHANISM, AND WHY NOT `POST /api/nodes`
+//   The obvious route is the one the persona/boot-counter write-backs already
+//   use, POST /api/nodes. It is the wrong instrument here, verified against the
+//   live engram binary in a sandbox:
+//     - it mints a NEW server-side id (engram_node), so the soul's id and the
+//       owner's id diverge — the next /api/sync pull re-imports the node as a
+//       DUPLICATE, and any edge referencing the soul's id never resolves;
+//     - it accepts only {content, node_type, salience} and drops label, tier,
+//       tags, importance, confidence, metadata. A probe posted with tier
+//       "Canonical" came back tier "Working", importance 0.5.
+//   POST /api/load-merge (Will's own route, el `dc39a61`) is the right one:
+//     - engram_load_merge PRESERVES the id and every field;
+//     - it dedups nodes by id and edges by (from_id,to_id,relation), so a
+//       re-submitted delta is a NO-OP — retry safety is free, and it is the same
+//       local-wins semantics the graph already uses;
+//     - it calls persist_canonical() — THE OWNER writes its own canonical file.
+//       The soul never touches it. The ownership rule is honoured in its
+//       strongest form rather than worked around;
+//     - it returns real counts {ok, nodes_added, edges_added, node_count},
+//       so a receipt can be a MEASUREMENT instead of a fixed success shape.
+//
+// SPOOL-AND-DRAIN, AND WHY IT IS NOT JUST A DIRECT POST
+//   Measured in a sandbox against a 79k-node / 176MB graph (live scale): one
+//   load-merge costs ~0.38s, essentially all of it the owner's persist_canonical.
+//   A chat turn writes 5-7 nodes; pushing each separately would add ~2.7s per
+//   turn. So writes are STAGED and pushed in one coalesced batch.
+//   The staging buffer is the FILESYSTEM, not process state, because the soul
+//   serves each HTTP connection on its own pthread (el_runtime http_serve_async)
+//   and a shared in-process buffer would lose entries to a read-modify-write
+//   race — silently, which is the one failure mode this file exists to end.
+//   One file per write, named with uuid_v4, is race-free by construction and
+//   buys a property a memory buffer cannot: writes that could not be pushed
+//   SURVIVE A SOUL CRASH and are drained on the next boot.
+//
+// WHAT IS DELIBERATELY NOT PUSHED
+//   - InternalStateEvent / heartbeat telemetry. Will's own carve-out, stated in
+//     engram server.el 8f8ccc9: "48h-pruned, loss-tolerant, ~2/min; snapshotting
+//     28MB per heartbeat is waste."
+//   NOTE (ours, flagged for Will): we do NOT additionally exclude Working-tier
+//   nodes. That exclusion exists in `fb0bb55` to stop the boot counter leaking
+//   through the /api/sync PULL; it is about sync backflow, not durability.
+//   Applying it here would exclude mem_store — which writes tier "Working" — and
+//   mem_store is the single most important durable write path in the soul. Boot
+//   seeding reads the canonical file wholesale, so a pushed Working-tier node
+//   does survive restart. This is the one classification call this file makes
+//   that Will has not ruled on.
+//
+// WHAT THIS BOUNDARY CANNOT EXPRESS (by construction, not by omission)
+//   - engram_strengthen (salience/activation drift): load-merge SKIPS ids that
+//     already exist, so it cannot update an existing node. There is no owner-side
+//     update/upsert route. Not pushable through any current route; left as a
+//     follow-up that needs a change in the engram repo.
+//   - engram_forget (hard delete): load-merge is additive and has no delete verb.
+//     Propagating deletes would mean DELETE /api/nodes/<id>, a HARD delete at the
+//     owner — which scripts/verify-soul-contract.sh section B explicitly fails the
+//     build for ("to delete is to supersede/tombstone, never hard-remove"). Local
+//     deletes therefore stay local; the TOMBSTONE NODE and its "tombstones" edge
+//     (mem_tombstone) are pushed, and that is the sanctioned representation of a
+//     deletion in this graph.
+
+// ── Configuration ─────────────────────────────────────────────────────────────
+
+// wt_engram_url — same resolution order as ise_post: env, then the state key
+// stashed at boot. NO hardcoded localhost fallback: unlike telemetry, inventing
+// a destination for durable data would risk pushing a user's memories at whatever
+// happens to be listening on 8742. Empty means "no HTTP owner" -> file mode.
+fn wt_engram_url() -> String {
+    let env_url: String = env("ENGRAM_URL")
+    if !str_eq(env_url, "") { return env_url }
+    return state_get("soul_engram_url")
+}
+
+fn wt_api_key() -> String {
+    let env_key: String = env("ENGRAM_API_KEY")
+    if !str_eq(env_key, "") { return env_key }
+    return state_get("soul_engram_api_key")
+}
+
+// wt_enabled — true only in HTTP-engram mode. In file mode the soul IS the
+// persistence owner and every path below is a no-op, so this whole feature is
+// inert for genesis/local deployments. That is also what makes it reversible.
+fn wt_enabled() -> Bool {
+    return !str_eq(wt_engram_url(), "")
+}
+
+// wt_spool_dir — where staged deltas live. MUST be readable by the engram
+// process: /api/load-merge takes a PATH and the owner opens it itself. Both
+// processes are same-host by construction (dev-stack LaunchAgents; the GKE
+// image starts engram and soul in one container per entrypoint.sh).
+fn wt_spool_dir() -> String {
+    let raw: String = env("SOUL_OUTBOX_DIR")
+    let dir: String = if str_eq(raw, "") { env("HOME") + "/.neuron/soul-outbox" } else { raw }
+    fs_mkdir(dir)
+    return dir
+}
+
+// ── Helpers ───────────────────────────────────────────────────────────────────
+
+// wt_esc — minimal JSON string escape. Deliberately local rather than reusing
+// chat.el's json_safe: persist.el is imported BY memory.el, which is imported by
+// chat.el, so depending on chat.el here would be an import cycle.
+fn wt_esc(s: String) -> String {
+    let s1: String = str_replace(s, "\\", "\\\\")
+    let s2: String = str_replace(s1, "\"", "\\\"")
+    let s3: String = str_replace(s2, "\n", "\\n")
+    let s4: String = str_replace(s3, "\r", "\\r")
+    let s5: String = str_replace(s4, "\t", "\\t")
+    return s5
+}
+
+// wt_durable_class — Will's telemetry carve-out, by node_type. See header.
+fn wt_durable_class(node_type: String) -> Bool {
+    if str_eq(node_type, "InternalStateEvent") { return false }
+    return true
+}
+
+// wt_inner — strip the surrounding brackets off a JSON array so several arrays
+// can be concatenated into one. Returns "" for "[]" / "" / anything too short.
+fn wt_inner(arr: String) -> String {
+    let n: Int = str_len(arr)
+    if n < 3 { return "" }
+    if !str_starts_with(arr, "[") { return "" }
+    return str_slice(arr, 1, n - 1)
+}
+
+// wt_read — fs_read, plus a MANDATORY reset of the runtime's binary-length hint.
+//
+// THIS IS NOT OPTIONAL AND MUST NOT BE "SIMPLIFIED" BACK TO A BARE fs_read.
+// The pinned runtime (vendor/el-runtime/v1.0.0-20260501) keeps a thread-local
+// `_tl_fs_read_len` that fs_read SETS to the file's byte count (so binary files
+// can be served with a correct Content-Length) and that http_send_response
+// CONSUMES as the Content-Length of the next reply. Nothing else clears it
+// except json_get_raw. So any fs_read during request handling that is not
+// followed by a json_get_raw makes the NEXT HTTP response advertise the FILE's
+// length instead of the body's — and the runtime then sends that many bytes,
+// appending whatever adjacent heap memory follows the reply.
+//
+// Caught here, measured: a /api/neuron/memory reply that should be 86 bytes went
+// out as 497, with 411 bytes of this module's own spool paths and log strings
+// trailing the JSON. The drain reads spool files mid-request, so this boundary
+// is exactly where the landmine gets stepped on.
+//
+// Upstream el fixed the class in `43636ae` ("pair fs_read length hint with its
+// buffer"); that runtime is NOT the one vendored here, and re-pinning the
+// runtime is deliberately out of scope for this change. Clearing the hint at
+// our own boundary fixes our exposure without touching the pinned C.
+// json_get_raw is used as the reset because it is the only builtin in this
+// runtime that zeroes the hint, and it does so before any early return.
+fn wt_clear_binlen() -> Void {
+    let discard: String = json_get_raw("{}", "_wt_reset")
+}
+
+fn wt_read(path: String) -> String {
+    let data: String = fs_read(path)
+    wt_clear_binlen()
+    return data
+}
+
+// wt_sweep — best-effort removal of the zero-byte husks left by truncation.
+// The runtime exposes no unlink builtin, so a drained delta is emptied rather
+// than deleted; this reclaims the directory entries.
+//
+// `-empty` is the safety property, not an optimisation: the command is
+// STRUCTURALLY INCAPABLE of removing a delta that still has content, so it can
+// never destroy a pending write even if it runs concurrently with a stage.
+// Only the directory path is interpolated (never a filename), and it is quoted.
+// The exit code is ignored — an un-swept husk costs one directory entry.
+fn wt_sweep(dir: String) -> Void {
+    if str_eq(dir, "") { return }
+    if str_contains(dir, "'") { return }
+    exec_command("find '" + dir + "' -maxdepth 1 -name 'wt*.json' -empty -delete 2>/dev/null")
+}
+
+// ── Staging ───────────────────────────────────────────────────────────────────
+
+// wt_stage — write ONE delta file. uuid_v4 in the name makes concurrent stagers
+// collision-free without any lock. Returns true if the delta is on disk.
+fn wt_stage(nodes_json: String, edges_json: String) -> Bool {
+    let dir: String = wt_spool_dir()
+    if str_eq(dir, "") { return false }
+    let payload: String = "{\"nodes\":" + nodes_json + ",\"edges\":" + edges_json + "}"
+    let path: String = dir + "/wt-" + uuid_v4() + ".json"
+    fs_write(path, payload)
+    // Read-back-verify the stage itself. A stage that did not land is a write we
+    // would otherwise believe was queued — exactly the hallucinated-save class.
+    if str_eq(wt_read(path), "") {
+        println("[persist] wt_stage: FAILED to write spool file " + path + " — delta not queued")
+        return false
+    }
+    return true
+}
+
+// ── The write boundary ────────────────────────────────────────────────────────
+
+// wt_node — create a node locally AND queue it for the persistence owner.
+// Same signature and same return contract as engram_node_full ("" on failure),
+// so converting a call site is a rename and nothing else.
+fn wt_node(content: String, node_type: String, label: String,
+           salience: Float, importance: Float, confidence: Float,
+           tier: String, tags: String) -> String {
+    let id: String = engram_node_full(content, node_type, label,
+                                      salience, importance, confidence,
+                                      tier, tags)
+    if str_eq(id, "") { return "" }
+    // engram_get_node_json emits the SAME record shape engram_save writes (minus
+    // the embedding vector, which the owner backfills lazily), so the read-back
+    // doubles as the delta payload — no second serialization to drift.
+    let rec: String = engram_get_node_json(id)
+    if str_eq(rec, "") || str_eq(rec, "{}") {
+        println("[persist] wt_node: local write did not read back, id=" + id + " label=" + label)
+        return ""
+    }
+    if wt_enabled() && wt_durable_class(node_type) {
+        wt_stage("[" + rec + "]", "[]")
+    }
+    return id
+}
+
+// wt_edge — create an edge locally AND queue it. Mirrors engram_connect.
+//
+// The edge id is freshly generated rather than read back: the runtime exposes no
+// "id of the edge I just created" accessor, and the owner dedups edges by
+// (from_id,to_id,relation), never by id — so the id is not load-bearing. The
+// consequence, stated plainly: the soul's copy and the owner's copy of the same
+// edge carry different edge ids. Nothing in either codebase looks an edge up by
+// id (neighbors traversal scans from_id/to_id), so this is cosmetic.
+fn wt_edge(from_id: String, to_id: String, weight: Float, relation: String) -> Void {
+    engram_connect(from_id, to_id, weight, relation)
+    if !wt_enabled() { return }
+    if str_eq(from_id, "") || str_eq(to_id, "") { return }
+    let ts: Int = time_now()
+    let rec: String = "{\"id\":\"" + uuid_v4() + "\""
+        + ",\"from_id\":\"" + wt_esc(from_id) + "\""
+        + ",\"to_id\":\"" + wt_esc(to_id) + "\""
+        + ",\"relation\":\"" + wt_esc(relation) + "\""
+        + ",\"metadata\":\"{}\""
+        + ",\"weight\":" + float_to_str(weight)
+        + ",\"confidence\":1"
+        + ",\"created_at\":" + int_to_str(ts)
+        + ",\"updated_at\":" + int_to_str(ts)
+        + ",\"last_fired\":0,\"inhibitory\":0,\"layer_id\":1}"
+    wt_stage("[]", "[" + rec + "]")
+}
+
+// ── The drain ─────────────────────────────────────────────────────────────────
+
+// wt_drain — coalesce every staged delta into ONE load-merge against the owner.
+//
+// Returns: nodes_added on success (>= 0), 0 when there was nothing to do, and
+// -1 when the push FAILED. -1 is load-bearing: on failure the spool files are
+// left untouched, so nothing is lost and the next drain retries them. A caller
+// must never read a non-negative return as "my particular node is durable" —
+// use wt_durable(id) for that.
+//
+// Concurrency: several threads may drain at once. Each builds its own batch file
+// (uuid-named), and overlapping batches are harmless because load-merge dedups.
+// Files are truncated ONLY after a confirmed ok:true, so a lost race costs a
+// redundant push, never a dropped write.
+fn wt_drain() -> Int {
+    if !wt_enabled() { return 0 }
+    let dir: String = wt_spool_dir()
+    if str_eq(dir, "") { return 0 }
+
+    // el_list_len/el_list_get, NOT json_stringify(fs_list(...)): fs_list builds
+    // a native list via el_list_append, and json_stringify does not serialize
+    // that type — it renders the raw pointer value. (Verified in isolation; the
+    // same latent defect is live in studio.el's /api/tools/file/list route,
+    // which returns e.g. {"entries":4386409744}. Noted, not fixed here.)
+    let listing = fs_list(dir)
+    let count: Int = el_list_len(listing)
+    if count == 0 { return 0 }
+
+    let nodes_acc: String = ""
+    let edges_acc: String = ""
+    let drained: String = ""
+    let found: Int = 0
+    let i: Int = 0
+    // No `continue` / `break`: elc lists them as keywords but not one line of
+    // the shipped soul uses either, so they are unexercised on this build path.
+    // Guard conditions are expressed as nested ifs instead, and every rebind is
+    // at the loop-body top level where `let x = ...` is assignment (the idiom
+    // memory.el's boot-counter loop relies on) — never inside a nested block,
+    // where it would shadow instead.
+    while i < count {
+        let name: String = el_list_get(listing, i)
+        // A delta is only usable when it ends with the closing "]}" that
+        // wt_stage writes last. fs_write is not atomic, so a file being written
+        // right now can be observed half-formed; requiring the terminator means
+        // it is picked up whole on the next drain instead of merged as garbage.
+        // An empty read means "already drained and truncated" — not an error.
+        let p: String = if str_starts_with(name, "wt-") { dir + "/" + name } else { "" }
+        let raw: String = if str_eq(p, "") { "" } else { wt_read(p) }
+        let usable: Bool = !str_eq(raw, "") && str_ends_with(raw, "]}")
+        let nj: String = if usable { wt_inner(json_get_raw(raw, "nodes")) } else { "" }
+        let ej: String = if usable { wt_inner(json_get_raw(raw, "edges")) } else { "" }
+        let nodes_acc = if str_eq(nj, "") { nodes_acc } else if str_eq(nodes_acc, "") { nj } else { nodes_acc + "," + nj }
+        let edges_acc = if str_eq(ej, "") { edges_acc } else if str_eq(edges_acc, "") { ej } else { edges_acc + "," + ej }
+        let drained = if !usable { drained } else if str_eq(drained, "") { p } else { drained + "\n" + p }
+        let found = if usable { found + 1 } else { found }
+        let i = i + 1
+    }
+
+    if found == 0 { return 0 }
+
+    let combined: String = "{\"nodes\":[" + nodes_acc + "],\"edges\":[" + edges_acc + "]}"
+    let batch: String = dir + "/wtb-" + uuid_v4() + ".json"
+    fs_write(batch, combined)
+    if str_eq(wt_read(batch), "") {
+        println("[persist] wt_drain: could not write batch file " + batch + " — " + int_to_str(found) + " deltas stay queued")
+        return -1
+    }
+
+    let url: String = wt_engram_url()
+    let key: String = wt_api_key()
+    let body: String = "{\"path\":\"" + wt_esc(batch) + "\",\"_auth\":\"" + wt_esc(key) + "\"}"
+    let resp: String = http_post_json(url + "/api/load-merge", body)
+
+    // The batch file is pure scratch — the retry is rebuilt from the SPOOL, not
+    // from it. Truncate it unconditionally, before branching on the outcome, so
+    // a persistently unreachable owner cannot accumulate one husk per attempt.
+    fs_write(batch, "")
+
+    // Distinguish the two failures rather than collapsing them: "cannot reach
+    // the owner" and "the owner refused this delta" need different human
+    // responses, and a log line that says the wrong one costs a debugging hour.
+    // curl surfaces transport errors as a JSON body, so an empty response is not
+    // the only unreachable signal.
+    // (str_contains rather than a strict parse on purpose — the engram's HTTP
+    //  responses have been observed carrying trailing bytes past the JSON.)
+    let unreachable: Bool = str_eq(resp, "")
+        || str_contains(resp, "Couldn't connect")
+        || str_contains(resp, "Failed to connect")
+        || str_contains(resp, "Could not resolve")
+        || str_contains(resp, "timed out")
+    if unreachable {
+        wt_sweep(dir)
+        println("[persist] wt_drain: owner UNREACHABLE at " + url + " — " + int_to_str(found)
+            + " deltas stay queued in " + dir + " (will retry): " + resp)
+        return -1
+    }
+    if !str_contains(resp, "\"ok\":true") {
+        wt_sweep(dir)
+        println("[persist] wt_drain: owner REJECTED the delta — " + int_to_str(found)
+            + " stay queued in " + dir + ": " + resp)
+        return -1
+    }
+
+    let added: Int = json_get_int(resp, "nodes_added")
+    let added_e: Int = json_get_int(resp, "edges_added")
+
+    // Confirmed. Truncate the drained spool files so they are not re-pushed.
+    // Truncation (not deletion) because the runtime exposes no unlink builtin;
+    // an emptied file is inert to the loop above. The zero-byte husks are then
+    // swept below.
+    let paths = str_split(drained, "\n")
+    let pn: Int = el_list_len(paths)
+    let k: Int = 0
+    while k < pn {
+        let one: String = el_list_get(paths, k)
+        if !str_eq(one, "") { fs_write(one, "") }
+        let k = k + 1
+    }
+    wt_sweep(dir)
+
+    println("[persist] wt_drain: pushed " + int_to_str(found) + " deltas -> owner added "
+        + int_to_str(added) + " nodes, " + int_to_str(added_e) + " edges")
+    return added
+}
+
+// wt_durable — is this id present AT THE OWNER? The only honest answer to
+// "did my write persist" in HTTP mode.
+//
+// In file mode the soul IS the owner, so the local read-back is the owner-side
+// read-back and this collapses to the pre-existing check.
+//
+// nodes_added from wt_drain is NOT a substitute: a concurrent drain may have
+// already pushed this node, making our own added count 0 while the node is
+// perfectly durable. Presence at the owner is the fact; counts are telemetry.
+fn wt_durable(id: String) -> Bool {
+    if str_eq(id, "") { return false }
+    if !wt_enabled() {
+        let local: String = engram_get_node_json(id)
+        return !str_eq(local, "") && !str_eq(local, "null") && !str_eq(local, "{}")
+    }
+    let url: String = wt_engram_url()
+    let resp: String = http_get(url + "/api/nodes/" + id)
+    if str_eq(resp, "") { return false }
+    if str_eq(resp, "{}") { return false }
+    return str_contains(resp, "\"id\"")
+}
+
+// wt_commit — flush, then assert at the owner. The receipt callers should use.
+// Deliberately NOT a fixed success shape: it can and does return false while the
+// local write is perfectly fine in RAM, which is the true state of affairs when
+// the owner is unreachable.
+fn wt_commit(id: String) -> Bool {
+    if str_eq(id, "") { return false }
+    if !wt_enabled() {
+        let local: String = engram_get_node_json(id)
+        return !str_eq(local, "") && !str_eq(local, "null") && !str_eq(local, "{}")
+    }
+    let pushed: Int = wt_drain()
+    return wt_durable(id)
+}

routes.el

@@ -15,6 +15,40 @@ fn flag_true(body: String, key: String) -> Bool {
     return json_get_bool(body, key) || json_get_int(body, key) > 0
 }
 
+// ---------------------------------------------------------------------------
+// plain_chat_envelope — the JSON response contract for a non-agentic ("Tools: Off")
+// chat turn. Every /api/chat dispatch that calls layered_cycle goes through here, so
+// the three call sites cannot drift apart.
+//
+// WHY THE ENVELOPE IS BUILT HERE AND NOT INSIDE layered_cycle:
+// layered_cycle returns the user-facing text AFTER safety_validate has acted on it.
+// Keeping the JSON out of the cycle means the output gate always sees raw model text
+// and never an escaped blob — there is nothing to unwrap and re-wrap on the crisis
+// path, which is exactly the failure mode that made wiring handle_chat unsafe.
+// Escaping is the last thing that happens, strictly after the gate.
+//
+// FIELDS: `reply` and `response` carry the same validated text. Both are required by
+// live clients — the desktop app reads `reply` first (DaemonClient.parseChatResponse),
+// while the CLI tools and the Telegram gateway read `response` (the gateway reads only
+// `response`). Emitting one would break the other.
+//
+// EMPTY MEANS FAILURE, NOT AN EMPTY ANSWER: a hard bell returns the fixed crisis
+// message and a soft bell is padded to non-empty by safety_validate, so the only way
+// an empty string leaves the cycle is a failed model call. It is reported as an error
+// rather than dressed up as a successful blank reply.
+// ---------------------------------------------------------------------------
+fn plain_chat_envelope(validated: String, model: String) -> String {
+    if str_eq(validated, "") {
+        return "{\"error\":\"llm unavailable\",\"reply\":\"\",\"response\":\"\",\"agentic\":false,\"tools_used\":[]}"
+    }
+    let safe: String = json_safe(validated)
+    return "{\"reply\":\"" + safe + "\""
+        + ",\"response\":\"" + safe + "\""
+        + ",\"model\":\"" + json_safe(model) + "\""
+        + ",\"agentic\":false"
+        + ",\"tools_used\":[]}"
+}
+
 // ---------------------------------------------------------------------------
 // Rate limiting — simple in-memory per-IP sliding window counter.
 //
@@ -152,7 +186,7 @@ fn route_imprint_contextual(body: String) -> String {
         return "{\"ok\":false,\"error\":\"empty body\"}"
     }
     let tags: String = "[\"imprint\",\"contextual\"]"
-    let id: String = engram_node_full(
+    let id: String = wt_node(
         body,
         "Entity",
         "imprint:contextual",
@@ -174,7 +208,7 @@ fn route_imprint_user(body: String) -> String {
         return "{\"ok\":false,\"error\":\"empty body\"}"
     }
     let tags: String = "[\"imprint\",\"user\"]"
-    let id: String = engram_node_full(
+    let id: String = wt_node(
         body,
         "Entity",
         "imprint:user",
@@ -205,7 +239,7 @@ fn route_synthesize(body: String) -> String {
     }
     let req: String = "synthesize " + parent_a + " " + parent_b
     let tags: String = "[\"soul-inbox-pending\",\"synthesis-request\"]"
-    engram_node_full(
+    wt_node(
         req,
         "Entity",
         "synthesis-request",
@@ -243,8 +277,14 @@ fn handle_dharma_recv(body: String) -> String {
         } else if agentic_flag {
             handle_chat_agentic(chat_body)
         } else {
-            let screened_reply: String = layered_cycle(raw_msg)
-            screened_reply
+            // Non-agentic ("Tools: Off"): the full L1→L2→L3→L1 cycle, which now generates
+            // at L3 instead of echoing. Envelope built outside the cycle — see
+            // plain_chat_envelope.
+            // FIX B/E1 (2026-08-05): the cycle is told which conversation it is in, and
+            // whether this generation is conversation at all. Same two arguments at all
+            // three dispatch sites.
+            let screened_reply: String = layered_cycle(raw_msg, json_get(chat_body, "session_id"), is_utility_request(chat_body, json_get(chat_body, "session_id")))
+            plain_chat_envelope(screened_reply, chat_default_model())
         }
         auto_persist(chat_body, reply)
         return reply
@@ -355,7 +395,28 @@ fn handle_connectors(method: String, clean: String, body: String) -> String {
     return "{\"ok\":false,\"error\":\"unknown connectors route\"}"
 }
 
+// handle_request — the soul's HTTP entry point.
+//
+// NOTE ON THE NAME (neuron#117): the el runtime resolves this handler by NAME
+// via dlsym(RTLD_DEFAULT, "handle_request") — that is why the Linux build must
+// link -rdynamic. So the dispatcher body moved to route_dispatch and the name
+// `handle_request` stays put as a thin wrapper. Do not rename it back.
+//
+// The wrapper exists to give the write-through boundary a guaranteed flush
+// point. route_dispatch returns from ~60 places; a per-branch flush would be
+// forgotten on the 61st. Draining here means EVERY request that staged a write
+// pushes it before the connection closes, whatever route produced it, including
+// routes added later that know nothing about persistence.
+//
+// wt_drain is a no-op (no HTTP, no cost) when nothing is staged and when the
+// soul is not in HTTP-engram mode, so this is free on read traffic.
 fn handle_request(method: String, path: String, body: String) -> String {
+    let resp: String = route_dispatch(method, path, body)
+    let flushed: Int = wt_drain()
+    return resp
+}
+
+fn route_dispatch(method: String, path: String, body: String) -> String {
     let clean: String = strip_query(path)
 
     // ACTIVITY STAMP (2026-07-30 self-review): every inbound HTTP request —
@@ -392,10 +453,27 @@ fn handle_request(method: String, path: String, body: String) -> String {
             return engram_scan_nodes_json(9999, 0)
         }
         if str_eq(clean, "/api/graph/edges") {
-            // TODO(reliability #8): engram_save races with awareness loop mem_save().
-            // Both now use atomic write-to-temp+rename (el_runtime.c). Serialised
-            // by engram_global_mu. Future: add engram_edges_json() builtin.
-            let snap_path: String = env("HOME") + "/.neuron/engram/snapshot.json"
+            // FIXED (neuron#117): this GET used to engram_save() straight over
+            // ~/.neuron/engram/snapshot.json — a READ route, in a process that is
+            // NOT the persistence owner, overwriting the owner's canonical file
+            // on every call. It broke soul.el:571-573 ("the soul must NEVER write
+            // to the local snapshot") and it is the same defect class Will removed
+            // from the engram itself in el `dc39a61` ("stop read routes clobbering
+            // canonical snapshot"), where route_scan_edges/route_sync were moved
+            // to scratch paths for exactly this reason. It was also the race the
+            // old TODO(reliability #8) admitted to.
+            //
+            // Export to a scratch path instead. Same response, no canonical write.
+            // The soul's own snapshot writes are otherwise already gated behind
+            // state key "soul_snapshot_path", which is set ONLY in the genesis
+            // file-mode branch (soul.el: is_genesis && safe_to_seed, and
+            // safe_to_seed is unconditionally false when ENGRAM_URL is set) — so
+            // after this change the soul writes nothing at all in HTTP mode.
+            // Future: add an engram_edges_json() builtin and drop the file round
+            // trip entirely.
+            let scratch_dir: String = env("TMPDIR")
+            let scratch_base: String = if str_eq(scratch_dir, "") { "/tmp" } else { scratch_dir }
+            let snap_path: String = scratch_base + "/soul-edges-export-" + state_get("soul_cgi_id") + ".json"
             engram_save(snap_path)
             let snap: String = fs_read(snap_path)
             let edges_raw: String = json_get_raw(snap, "edges")
@@ -416,8 +494,11 @@ fn handle_request(method: String, path: String, body: String) -> String {
             } else if agentic_flag {
                 handle_chat_agentic(body)
             } else {
-                let screened_reply: String = layered_cycle(eff_msg)
-                screened_reply
+                // Non-agentic ("Tools: Off") — same cycle and same envelope as POST.
+                // FIX B/E1: same threading. A GET probe usually carries no session_id, which
+                // resolves to the anonymous window — the documented behaviour for this door.
+                let screened_reply: String = layered_cycle(eff_msg, json_get(body, "session_id"), is_utility_request(body, json_get(body, "session_id")))
+                plain_chat_envelope(screened_reply, chat_default_model())
             }
             auto_persist(body, reply)
             return reply
@@ -486,6 +567,13 @@ fn handle_request(method: String, path: String, body: String) -> String {
         if str_starts_with(clean, "/api/neuron/graph") {
             return handle_api_inspect_graph(method, path, body)
         }
+        // Stage 1 structural audit (CGI provisional, "Structural audit 430").
+        // GET because it is a read of the graph's own structure; the query string
+        // carries the sample caps (?edge_sample=, ?node_sample=, ?edges=0), so
+        // str_starts_with rather than str_eq.
+        if str_starts_with(clean, "/api/neuron/audit/structural") {
+            return handle_api_structural_audit(method, path, body)
+        }
         if str_starts_with(clean, "/api/neuron/list/") {
             // Offset 17 = len("/api/neuron/list/"). Was 16, which left a leading "/" on node_type
             // ("/BacklogItem"), so engram_scan_nodes_by_type_json matched nothing → list/<type>
@@ -580,8 +668,13 @@ fn handle_request(method: String, path: String, body: String) -> String {
             } else if agentic_flag {
                 handle_chat_agentic(body)
             } else {
-                let screened_reply: String = layered_cycle(raw_msg)
-                screened_reply
+                // Non-agentic ("Tools: Off") — the app's DEFAULT mode (AgentMode.NEVER).
+                // Full L1→L2→L3→L1 cycle with real generation at L3; envelope built
+                // outside the cycle so safety_validate always sees raw text.
+                // FIX B/E1: same threading. This is the app's main plain-chat door, so this
+                // is the site that ends the blank stare in practice.
+                let screened_reply: String = layered_cycle(raw_msg, json_get(body, "session_id"), is_utility_request(body, json_get(body, "session_id")))
+                plain_chat_envelope(screened_reply, chat_default_model())
             }
             auto_persist(body, reply)
             return reply
@@ -662,6 +755,12 @@ fn handle_request(method: String, path: String, body: String) -> String {
         if str_eq(clean, "/api/neuron/graph/link") {
             return handle_api_link_entities(body)
         }
+        // POST accepted too: same handler, so a JSON-RPC-shaped caller that only
+        // speaks POST reaches the identical audit. Options still come from the
+        // query string — the handler reads no body fields.
+        if str_eq(clean, "/api/neuron/audit/structural") {
+            return handle_api_structural_audit(method, path, body)
+        }
         if str_eq(clean, "/api/neuron/memory") {
             return handle_api_remember(body)
         }

safety.el

@@ -204,7 +204,7 @@ fn safety_log_bell(level: String, reason: String, input_summary: String) -> Stri
     // Emit a fallback println so the bell event leaves at least a log trace even
     // when engram is degraded. This does not replace engram persistence -- it is a
     // last-resort audit trail when the primary write cannot be confirmed.
-    let node_id: String = engram_node_full(
+    let node_id: String = wt_node(
         content,
         "BellEvent",
         "bell:" + level,

scripts/run-el-test.sh

@@ -0,0 +1,108 @@
+#!/usr/bin/env bash
+# run-el-test.sh — compile and run one El test program from tests/.
+#
+# WHY THIS EXISTS (2026-08-07, issue #129):
+#   tests/ has held 14 test programs for months with no way to run them. CI does
+#   not run them. The convention printed in their own headers
+#   (`elc soul.el && ./soul --test tests/x.el`) refers to a --test flag the El
+#   runtime does not implement. So the tests were documentation, not gates —
+#   which is how a P0 safety regression shipped with a test directory present.
+#
+# THE RECIPE, AND WHY IT IS THIS SHAPE:
+#   Same discovery as gen-soul-amalgam.sh — `elc --target=c` emits only an extern
+#   prototype for any module that has a .elh header next to it, and inlines the
+#   module's bodies when it does not. A test that imports ../chat.el therefore
+#   compiles to a 18 KB unit full of unresolved externs unless the headers are
+#   out of the way. So: copy the sources into a scratch tree, delete every .elh
+#   on the import chain, and compile the test there.
+#
+#   Scratch copy on purpose: the worktree is shared with other terminals and
+#   deleting headers in place would be a shared-tree mutation with no owner.
+#
+# EXIT STATUS IS THE GATE: non-zero if the binary fails to build, crashes, or if
+# its output contains a FAIL line or reports a non-zero failed count. Do not
+# "improve" this into something that only checks the exit code of the test
+# binary — these El tests print failures and still exit 0.
+#
+# usage: scripts/run-el-test.sh tests/test_history_amplification.el
+set -euo pipefail
+
+TEST_REL="${1:?usage: run-el-test.sh tests/<test>.el}"
+SRC="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+TEST_NAME="$(basename "$TEST_REL" .el)"
+
+ELC="${ELC:-$HOME/neuron-dev-stack/src/el/lang/dist/platform/elc}"
+[ -x "$ELC" ] || ELC="$HOME/el-sdk/elc"
+[ -x "$ELC" ] || { echo "[run-el-test] FAIL: no elc found (set ELC=)"; exit 1; }
+
+RTC="${RTC:-$SRC/vendor/el-runtime/v1.0.0-20260501/el_runtime.c}"
+[ -f "$RTC" ] || RTC="$HOME/el-sdk/el_runtime.c"
+[ -f "$RTC" ] || { echo "[run-el-test] FAIL: no el_runtime.c found (set RTC=)"; exit 1; }
+RTDIR="$(dirname "$RTC")"
+
+EL_REPO="${EL_REPO:-$HOME/Development/neuron-technologies/el}"
+SSL="${SSL_PREFIX:-/opt/homebrew/opt/openssl@3}"
+
+GEN="$(mktemp -d "${TMPDIR:-/tmp}/el-test.XXXXXX")"
+trap 'rm -rf "$GEN"' EXIT
+
+mkdir -p "$GEN/neuron/tests" "$GEN/foundation/el/elp/src"
+cp "$SRC"/*.el "$GEN/neuron/"
+cp "$SRC"/tests/*.el "$GEN/neuron/tests/" 2>/dev/null || true
+[ -d "$EL_REPO/elp/src" ] && cp "$EL_REPO"/elp/src/*.el "$GEN/foundation/el/elp/src/" 2>/dev/null || true
+# The whole recipe depends on there being no headers to short-circuit inlining.
+find "$GEN" -name '*.elh' -delete
+
+echo "[run-el-test] compiling $TEST_REL"
+( cd "$GEN/neuron" && "$ELC" --target=c "tests/${TEST_NAME}.el" ) > "$GEN/${TEST_NAME}.c"
+
+BODIES=$(grep -c '^el_val_t .*) {$' "$GEN/${TEST_NAME}.c" || true)
+echo "[run-el-test] $(wc -c < "$GEN/${TEST_NAME}.c" | tr -d ' ') bytes, ${BODIES} inlined function bodies"
+# A test that imports ../chat.el pulls in the bulk of the engine. A tiny body
+# count means an import was read from a header instead of inlined, and the test
+# would be exercising extern stubs rather than the real code.
+if [ "$BODIES" -lt 100 ]; then
+  echo "[run-el-test] FAIL: only $BODIES inlined bodies — an import was not inlined"
+  exit 1
+fi
+
+cc -O2 -DHAVE_CURL \
+   -I"$RTDIR" -I"$SSL/include" -L"$SSL/lib" \
+   "$GEN/${TEST_NAME}.c" "$RTC" \
+   -lssl -lcrypto -lcurl -lpthread -lm \
+   -o "$GEN/${TEST_NAME}" 2> "$GEN/cc.log" || {
+     echo "[run-el-test] FAIL: compile error"; tail -30 "$GEN/cc.log"; exit 1; }
+
+# arm64 pointer-truncation guard (cc-brain.sh's rule): an implicit declaration of
+# a runtime symbol truncates its returned pointer to 32 bits.
+if grep -E 'implicit.*(engram_|el_)' "$GEN/cc.log"; then
+  echo "[run-el-test] FAIL: implicit declarations of runtime symbols"; exit 1; fi
+
+# Throwaway HOME so a test can never read or write the live engram at ~/.neuron.
+TEST_HOME="$GEN/home"
+mkdir -p "$TEST_HOME"
+
+echo "[run-el-test] running $TEST_NAME"
+set +e
+HOME="$TEST_HOME" NEURON_HOME="$TEST_HOME/.neuron" "$GEN/${TEST_NAME}" 2>&1 | tee "$GEN/out.txt"
+RC=${PIPESTATUS[0]}
+set -e
+
+if [ "$RC" -ne 0 ]; then
+  echo "[run-el-test] FAIL: $TEST_NAME exited $RC (crash or abort)"
+  exit 1
+fi
+if grep -q "  FAIL:" "$GEN/out.txt"; then
+  echo "[run-el-test] FAIL: $TEST_NAME reported failing assertions"
+  exit 1
+fi
+if grep -qE '[1-9][0-9]* failed' "$GEN/out.txt"; then
+  echo "[run-el-test] FAIL: $TEST_NAME reported a non-zero failed count"
+  exit 1
+fi
+if ! grep -q "PASS:" "$GEN/out.txt"; then
+  echo "[run-el-test] FAIL: $TEST_NAME produced no assertions at all"
+  exit 1
+fi
+
+echo "[run-el-test] PASS: $TEST_NAME"

scripts/verify-soul-contract.sh

@@ -0,0 +1,261 @@
+#!/usr/bin/env bash
+# verify-soul-contract.sh — the soul contract gate.
+#
+# TERMINOLOGY (canonical): the ENGRAM is the brain — the memory/knowledge-graph
+# substrate. The binary this gate exercises is the SOUL — the runtime/reasoning
+# engine compiled from dist/soul.c that serves the /api/ surface. The app
+# (neuron-ui) bundles the soul binary at resources/<platform>/neuron.
+#
+# WHY THIS EXISTS
+#   For a while the soul binary was hand-dropped, and a stale one shipped: it
+#   404'd several capability routes the app calls (knowledge-graph node
+#   update/delete, live-run narration, safety-contact, ...). This gate makes
+#   shipping a stale soul IMPOSSIBLE. It has two enforced sections:
+#     A. PRESENCE   — every route the app calls must be ANSWERED (not 404, not
+#                     the el-runtime "no handler"). This is the packaging gate:
+#                     if it fails, do not package.
+#     B. IMMUTABILITY — engram nodes/memories are immutable by design. To
+#                     "update" is to create a NEW node + a supersede EDGE back to
+#                     the original; the original is KEPT. To "delete" is to
+#                     supersede/tombstone, never hard-remove. A soul that
+#                     hard-deletes an engram node is DEFECTIVE and fails the gate.
+#
+# SAFETY
+#   Never touches the live soul (:7770), live engram (:8742), or ~/.neuron.
+#   Boots on a throwaway port (default 7799) with HOME=$(mktemp -d), a throwaway
+#   engram snapshot, a non-genesis cgi id, no ENGRAM_URL (so it uses its own
+#   in-process store, never the live server), NEURON_API_URL pointed at a dead
+#   port, and no ANTHROPIC_API_KEY (so no probe triggers a real LLM call).
+#   Connectors proxy to a HARDCODED 127.0.0.1:7771 (no env override): those
+#   sub-routes are probed with GET, which the soul maps to a read-only
+#   connectd_get, so this gate never writes to a running connectd bridge.
+#
+# USAGE
+#   scripts/verify-soul-contract.sh <path-to-soul-binary> [port]
+#   exit 0 = all required routes answered AND no destructive engram mutation;
+#   non-zero = a route is missing (presence) or a mutation route hard-deletes.
+set -uo pipefail
+
+SOUL="${1:?usage: verify-soul-contract.sh <soul-binary> [port]}"
+PORT="${2:-7799}"
+
+if [ "$PORT" = "7770" ] || [ "$PORT" = "8742" ] || [ "$PORT" = "7771" ]; then
+  echo "REFUSING: port $PORT is a live service port. Use a throwaway port." >&2
+  exit 2
+fi
+if [ ! -x "$SOUL" ]; then echo "not executable: $SOUL" >&2; exit 2; fi
+
+BASE="http://127.0.0.1:$PORT"
+THROW_HOME="$(mktemp -d "${TMPDIR:-/tmp}/soul-contract-home.XXXXXX")"
+SOUL_LOG="$(mktemp "${TMPDIR:-/tmp}/soul-contract-log.XXXXXX")"
+SOUL_PID=""
+cleanup() {
+  [ -n "$SOUL_PID" ] && kill "$SOUL_PID" 2>/dev/null
+  [ -n "$SOUL_PID" ] && { sleep 0.3; kill -9 "$SOUL_PID" 2>/dev/null; }
+  rm -rf "$THROW_HOME" "$SOUL_LOG"
+}
+trap cleanup EXIT INT TERM
+
+# =============================================================================
+# THE CONTRACT — routes the app (neuron-ui/src/main/kotlin/ai/neuron/ui/*.kt)
+# calls against the soul ($SOUL). Format: "METHOD PATH".
+#
+# EXCLUDED and why:
+#   /api/auth, /api/auth/status, /api/dispatch, /api/tasks
+#       -> served by the APP's own DispatchServer.kt (localhost:8080), not the
+#          soul. Not soul routes.
+#   /api/tags
+#       -> not handled by any soul .el (app-side/other). Pre-verified excluded.
+#   /api/neuron/, /api/neuron/node/, /api/connectors/ (bare prefixes)
+#       -> base-path string constants used to build the concrete routes below.
+#
+# KNOWN-PENDING (probed + reported, NON-blocking):
+#   POST /api/engram/import  -> the app's "Restore memory" path. No soul handler
+#       yet, and the app hides Restore from shipped builds (B3, "lands in an
+#       update"). Reported so we see it; does not block packaging.
+#
+# Connectors sub-routes are listed as GET (see SAFETY note): handle_connectors is
+# monolithic, so a GET reaching it proves the whole connectors surface without
+# writing to the live bridge. Binary-strings cross-check confirms each POST
+# sub-path literal is compiled in.
+# =============================================================================
+REQUIRED=(
+  "GET  /api/graph/nodes"
+  "GET  /api/graph/edges"
+  "POST /api/chat"
+  "GET  /api/config"
+  "POST /api/see"
+  "GET  /api/connectors"
+  "GET  /api/connectors/add"
+  "GET  /api/connectors/toggle"
+  "GET  /api/connectors/auto-approve"
+  "GET  /api/connectors/remove"
+  "GET  /api/connectors/secret"
+  "GET  /api/connectors/oauth/start"
+  "GET  /api/connectors/call"
+  "POST /api/neuron/memory"
+  "POST /api/neuron/memory/update"
+  "POST /api/neuron/memory/delete"
+  "POST /api/neuron/node/create"
+  "POST /api/neuron/node/update"
+  "POST /api/neuron/node/delete"
+  "POST /api/neuron/knowledge/capture"
+  "POST /api/neuron/knowledge/evolve"
+  "POST /api/neuron/knowledge/promote"
+  "POST /api/neuron/processes/define"
+  "GET  /api/run-progress/__contract_probe__"
+  "GET  /api/safety-contact"
+  "POST /api/safety-contact"
+  "GET  /api/sessions/__contract_probe__"
+)
+KNOWN_PENDING=(
+  "POST /api/engram/import"
+)
+
+# --- boot the soul -----------------------------------------------------------
+# Preserve the ambient environment (PATH, LD_LIBRARY_PATH, TMPDIR) so the
+# dynamically-linked soul finds its libs on any runner — using `env -i` here
+# stripped the library path on the Linux CI runner and the soul never booted.
+# Isolation is still guaranteed by UNSETTING the live-service vars (so it can
+# never reach the real engram/axon or make an LLM call) and by pointing HOME +
+# the snapshot at throwaway paths and the axon at a dead port.
+#
+# ISOLATION FIX (2026-08-03): unsetting ENGRAM_URL/SOUL_ENGRAM_URL is NOT enough.
+# The periodic engram sync (awareness.el) resolves its source as
+#   env(SOUL_ISE_URL)  ->  state(soul_engram_url)  ->  DEFAULT http://localhost:8742
+# so with those vars unset it silently pulls the LIVE engram (:8742) if that
+# server is up — the throwaway graph ballooned 56 -> 12k live nodes within
+# seconds, and the concurrent live-sync mutation both (a) broke test determinism
+# (the low-salience tombstone marker fell past the 9999 scan cap) and (b) meant
+# the "isolated" gate was reading the operator's live brain. Pin SOUL_ISE_URL to
+# the dead axon port so the sync target is unreachable: the soul stays on its own
+# in-process store, the gate is genuinely isolated, and Section B is deterministic.
+echo "== booting soul: $SOUL on port $PORT (throwaway HOME=$THROW_HOME) =="
+env \
+  -u ENGRAM_URL -u ENGRAM_API_KEY -u SOUL_ENGRAM_URL \
+  -u ANTHROPIC_API_KEY -u NEURON_LLM_API_KEY -u SOUL_IDENTITY \
+  HOME="$THROW_HOME" \
+  NEURON_PORT="$PORT" \
+  SOUL_CGI_ID="ntn-contract-$$" \
+  SOUL_ENGRAM_PATH="$THROW_HOME/throwaway-snapshot.json" \
+  NEURON_API_URL="http://127.0.0.1:9" \
+  SOUL_ISE_URL="http://127.0.0.1:9" \
+  SOUL_TICK_MS="3600000" SOUL_HEARTBEAT_MS="3600000" SOUL_REFRESH_MS="3600000" \
+  "$SOUL" >"$SOUL_LOG" 2>&1 &
+SOUL_PID=$!
+
+UP=0
+for _ in $(seq 1 60); do
+  if ! kill -0 "$SOUL_PID" 2>/dev/null; then
+    echo "!! soul exited during boot. log tail:" >&2; tail -20 "$SOUL_LOG" >&2; exit 3
+  fi
+  RSS=$(ps -o rss= -p "$SOUL_PID" 2>/dev/null | tr -d ' ')
+  if [ -n "$RSS" ] && [ "$RSS" -gt $((3*1024*1024)) ]; then
+    echo "!! soul RSS >3GB — kill -9" >&2; kill -9 "$SOUL_PID" 2>/dev/null; exit 3
+  fi
+  [ "$(curl -s -o /dev/null -w '%{http_code}' -m 2 "$BASE/health" 2>/dev/null)" = "200" ] && { UP=1; break; }
+  sleep 0.5
+done
+[ "$UP" = 1 ] || { echo "!! soul never healthy on $BASE/health" >&2; tail -20 "$SOUL_LOG" >&2; exit 3; }
+echo "== soul healthy =="; echo
+
+# --- probing helpers ---------------------------------------------------------
+# request METHOD PATH [BODY] -> prints response body (single line)
+request() {
+  curl -s -m 12 -X "$1" -H 'Content-Type: application/json' --data "${3:-{}}" "$BASE$2" 2>/dev/null | tr -d '\n'
+}
+# is_missing BODY -> 0 if the body is a "route not present" signal
+is_missing() {
+  printf '%s' "$1" | grep -qE '"error":"not found"|"code":"not_found"|no http handler registered|"code":"method_not_allowed"'
+}
+extract_id() { printf '%s' "$1" | grep -oE '"id":"[^"]+"' | head -1 | sed 's/.*"id":"//;s/"//'; }
+# BY-ID immutability verification (#199 by-id gate).
+# The prior check grepped /api/graph/nodes, i.e. engram_scan_nodes_json(9999,0):
+# a whole-graph dump. On a genesis-seeded throwaway engram that list is both
+# huge (multi-MB, full node content + embeddings) AND capped at 9999 nodes in
+# salience order. The tombstone MARKER is written at salience 0.01, so it sorts
+# dead last — and once the seeded graph approaches/exceeds the cap the marker
+# falls off the end of the list entirely (or is lost to transport truncation on
+# the ~10MB body). The normal-salience original still sorts early and survives,
+# which is why a correctly-tombstoning soul false-reported "kept but no tombstone
+# marker". Fix: verify BY ID via /api/neuron/graph?id=<id>&depth=1
+# (engram_neighbors_json, direction "both"), a compact ~900B neighborhood that is
+# independent of total graph size. The node itself proves KEPT; the incoming
+# "tombstones" edge surfaces the "tombstone:<id>" marker. Pass/fail semantics are
+# unchanged and strictly no weaker: a hard-delete leaves no by-id node (DESTROYED)
+# and a no-op delete leaves no marker (NO-OP) — both still fail. Verified: a
+# never-created id returns neither node nor marker.
+node_present() { # id -> 0 if the node still resolves by-id (KEPT), non-zero if hard-removed
+  request GET "/api/neuron/graph?id=$1&depth=1" | grep -qF "\"$1\""
+}
+
+# --- SECTION A: presence -----------------------------------------------------
+run_presence() {
+  local -n arr=$1; local fail=0
+  printf '  %-8s %-42s %s\n' "METHOD" "ROUTE" "RESULT"
+  for e in "${arr[@]}"; do
+    local m p body; m=$(awk '{print $1}' <<<"$e"); p=$(awk '{print $2}' <<<"$e")
+    body=$(request "$m" "$p")
+    if is_missing "$body"; then
+      printf '  %-8s %-42s MISSING  %s\n' "$m" "$p" "$(cut -c1-46 <<<"$body")"; fail=$((fail+1))
+    else
+      printf '  %-8s %-42s ANSWERED %s\n' "$m" "$p" "$(cut -c1-46 <<<"$body")"
+    fi
+  done
+  return $fail
+}
+
+echo "== SECTION A: PRESENCE (required, blocking) =="
+run_presence REQUIRED; A_FAIL=$?
+echo
+echo "== KNOWN-PENDING (non-blocking) =="
+run_presence KNOWN_PENDING; P_FAIL=$?
+echo
+
+# --- SECTION B: immutability (engram write routes must supersede, not destroy) --
+# For each mutation route: create a node, mutate it, then check the ORIGINAL id
+# still exists in the graph. KEPT = supersede/tombstone (correct). DESTROYED =
+# hard delete (DEFECTIVE -> fail). N/A = mutate route absent (a presence failure).
+# For "delete" mutations we additionally require a real tombstone marker
+# (label "tombstone:<id>") so a no-op delete cannot false-pass as KEPT.
+marker_present() { # id -> 0 if a "tombstone:<id>" marker is wired to the node (by-id neighborhood)
+  request GET "/api/neuron/graph?id=$1&depth=1" | grep -qF "tombstone:$1"
+}
+immut_check() { # label KIND(update|delete) CREATE_PATH MUTATE_PATH
+  local label="$1" kind="$2" create="$3" mutate="$4"
+  local cbody id mb mbody
+  cbody=$(request POST "$create" "{\"content\":\"__immut_${label}__\",\"node_type\":\"Memory\",\"label\":\"contract:immut\"}")
+  id=$(extract_id "$cbody")
+  if [ -z "$id" ]; then printf '  %-14s SKELETON-FAIL  create returned no id: %s\n' "$label" "$(cut -c1-40 <<<"$cbody")"; return 2; fi
+  mb="{\"id\":\"$id\"}"; [ "$kind" = update ] && mb="{\"id\":\"$id\",\"content\":\"__immut_${label}_v2__\"}"
+  mbody=$(request POST "$mutate" "$mb")
+  if is_missing "$mbody"; then printf '  %-14s N/A            mutate route absent (see Section A)\n' "$label"; return 0; fi
+  if ! node_present "$id"; then
+    printf '  %-14s DESTROYED      original %s hard-removed  <== DEFECTIVE\n' "$label" "$id"; return 1
+  fi
+  if [ "$kind" = delete ] && ! marker_present "$id"; then
+    printf '  %-14s NO-OP          original %s kept but no tombstone marker  <== DEFECTIVE\n' "$label" "$id"; return 1
+  fi
+  local how="supersede edge"; [ "$kind" = delete ] && how="tombstoned + hidden from default list"
+  printf '  %-14s KEPT           original %s survived (%s)\n' "$label" "$id" "$how"; return 0
+}
+
+echo "== SECTION B: IMMUTABILITY (engram nodes must be superseded, never destroyed) =="
+B_FAIL=0
+immut_check "memory-update" update /api/neuron/memory      /api/neuron/memory/update || B_FAIL=$((B_FAIL+$?))
+immut_check "memory-delete" delete /api/neuron/memory      /api/neuron/memory/delete || B_FAIL=$((B_FAIL+$?))
+immut_check "node-update"   update /api/neuron/node/create /api/neuron/node/update   || B_FAIL=$((B_FAIL+$?))
+immut_check "node-delete"   delete /api/neuron/node/create /api/neuron/node/delete   || B_FAIL=$((B_FAIL+$?))
+immut_check "memory-forget" delete /api/neuron/memory      /api/neuron/memory/forget || B_FAIL=$((B_FAIL+$?))
+echo
+
+echo "============================================================"
+RC=0
+if [ "$A_FAIL" -gt 0 ]; then echo "PRESENCE:   FAIL — $A_FAIL required route(s) unanswered. Do NOT package."; RC=1
+  else echo "PRESENCE:   PASS — all ${#REQUIRED[@]} required routes answered."; fi
+if [ "$B_FAIL" -gt 0 ]; then echo "IMMUTABILITY: FAIL — $B_FAIL engram write route(s) hard-delete. DEFECTIVE soul."; RC=1
+  else echo "IMMUTABILITY: PASS — no engram write route hard-deletes."; fi
+[ "$P_FAIL" -gt 0 ] && echo "note: $P_FAIL known-pending route(s) unanswered (expected; non-blocking)."
+echo "============================================================"
+[ "$RC" = 0 ] && echo "GATE: PASS" || echo "GATE: FAIL"
+exit $RC

sessions.el

@@ -87,7 +87,7 @@ fn session_create(body: String) -> String {
     let folder: String = json_get(body, "folder")
     let content: String = session_make_content(id, title, ts, ts, folder)
     let tags: String = "[\"session\",\"session:meta\",\"Conversation\"]"
-    let node_id: String = engram_node_full(
+    let node_id: String = wt_node(
         content, "Conversation", "session:meta",
         el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
         "Episodic", tags
@@ -358,7 +358,7 @@ fn session_update_patch(session_id: String, body: String) -> String {
     let created_int: Int = str_to_int(old_created)
     let new_content: String = session_make_content(session_id, eff_title, created_int, ts, eff_folder)
     let tags: String = "[\"session\",\"session:meta\",\"Conversation\"]"
-    let new_node_id: String = engram_node_full(
+    let new_node_id: String = wt_node(
         new_content, "Conversation", "session:meta",
         el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
         "Episodic", tags
@@ -456,7 +456,7 @@ fn session_hist_save(session_id: String, hist: String) -> Void {
     // TODO(reliability #7): delete-then-insert is not atomic — concurrent saves for the
     // same session can produce orphan history nodes. State is primary truth; engram fallback.
     let tags: String = "[\"session\",\"session-history\",\"Conversation\"]"
-    let discard: String = engram_node_full(
+    let discard: String = wt_node(
         hist, "Conversation", "session:messages:" + session_id,
         el_from_float(0.6), el_from_float(0.6), el_from_float(0.9),
         "Episodic", tags
@@ -488,7 +488,7 @@ fn session_hist_save(session_id: String, hist: String) -> Void {
                 + " | ts:" + int_to_str(ts_now)
             let summary_tags: String = "[\"session-emotional-summary\",\"affective\",\"bell:" + eff_level + "\",\"BellEvent\"]"
             let summary_sal: String = if str_eq(eff_level, "hard") { el_from_float(0.95) } else { el_from_float(0.85) }
-            let sum_discard: String = engram_node_full(
+            let sum_discard: String = wt_node(
                 summary_content,
                 "BellEvent",
                 "session:emotional-summary",
@@ -529,7 +529,7 @@ fn session_hist_save(session_id: String, hist: String) -> Void {
             if !str_eq(ot_id, "") { engram_forget(ot_id) }
             let oti = oti + 1
         }
-        let discard_topic: String = engram_node_full(
+        let discard_topic: String = wt_node(
             topic_content, "Conversation", topic_label,
             el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
             "Episodic", topic_tags
@@ -582,7 +582,7 @@ fn session_update_meta_timestamp(session_id: String) -> Void {
     let created_int: Int = str_to_int(old_created)
     let new_content: String = session_make_content(session_id, old_title, created_int, ts, old_folder)
     let tags: String = "[\"session\",\"session:meta\",\"Conversation\"]"
-    let new_id: String = engram_node_full(
+    let new_id: String = wt_node(
         new_content, "Conversation", "session:meta",
         el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
         "Episodic", tags
@@ -629,7 +629,7 @@ fn session_auto_title(session_id: String, first_message: String) -> Void {
     let created_int: Int = str_to_int(old_created)
     let new_content: String = session_make_content(session_id, new_title, created_int, ts, old_folder)
     let tags: String = "[\"session\",\"session:meta\",\"Conversation\"]"
-    let new_id: String = engram_node_full(
+    let new_id: String = wt_node(
         new_content, "Conversation", "session:meta",
         el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
         "Episodic", tags
@@ -677,6 +677,11 @@ fn handle_session_approve(session_id: String, body: String) -> String {
     // path for all sessions created through handle_chat_agentic / agentic_loop.
     let bridge_blob: String = state_get("mcp_bridge:" + session_id)
     if !str_eq(bridge_blob, "") {
+        // BUG-LEAK fix (2026-07-16): the approved tool executes below via dispatch_tool,
+        // whose path/command guards read the shared workspace-root key. Re-assert THIS
+        // session's own root first — an approval must never execute under whatever root
+        // the last unrelated request left behind.
+        state_set("agent_workspace_root", state_get("agent_workspace_root_" + session_id))
         // For "always": record tool_name in the always-allow list before resuming.
         // The tool_name is not stored in the bridge blob (only tool_use_id is).
         // Accept it from the body so the client can pass it along.
@@ -708,7 +713,13 @@ fn handle_session_approve(session_id: String, body: String) -> String {
         // For builtin tools with no client-provided content: fall back to
         // dispatch_tool so those tools still execute correctly.
         let client_content: String = json_get(body, "content")
-        let use_client_content: Bool = !str_eq(client_content, "")
+        // BUG-6 fix (2026-07-17): the naive json_get scanner matches "content" ANYWHERE
+        // in the body — including INSIDE tool_input — so every approved write_file (whose
+        // input always carries a content field) was mistaken for client-executed, never
+        // dispatched, and narrated as done: a false receipt with no file on disk. Builtin
+        // tools now ALWAYS dispatch server-side; client content is only honored for
+        // non-builtin (MCP/client-executed) tools. Stricter only.
+        let use_client_content: Bool = !str_eq(client_content, "") && !is_builtin_tool(approve_tool_name)
         let use_dispatch: Bool = is_builtin_tool(approve_tool_name) && !use_client_content
         let raw_input: String = json_get_raw(body, "tool_input")
         let eff_input: String = if str_eq(raw_input, "") { "{}" } else { raw_input }

soul.el

@@ -379,9 +379,23 @@ fn emit_session_start_event() -> Void {
 // layered_cycle — routes user-facing requests through the 4-layer consciousness stack.
 // L0 (core) → L1 (safety screen) → L2a (continuity + behavioral profiling) → L2b (mission alignment) → L3 (imprint) → L1 (safety validate)
 // Internal cognition (heartbeat, proactive, memory ops) bypasses layers — use one_cycle directly.
-fn layered_cycle(raw_input: String) -> String {
-    let history: String = state_get("conv_history")
-    let session_id: String = state_get("current_session_id")
+//
+// FIX B (2026-08-05) — the cycle now knows which conversation it is in.
+//
+// session_id: the caller's session, threaded from the route. Was previously read from the
+// state key "current_session_id", which is read HERE and written NOWHERE in the entire
+// source — verified across every .el file. So this value was unconditionally "", and every
+// downstream consumer of it silently fell back to a process-global bucket: conversation
+// history, and the steward's continuity tracking (TODO reliability #4, below, describes the
+// cross-session bleed this caused; threading the real id closes it). The plain path's blank
+// stare and the agentic path's scoped history were the same defect seen from two sides.
+//
+// utility: true when the generation is not part of the user's conversation — the app's
+// title and insight passes. Answered normally, never recorded. See is_utility_request.
+fn layered_cycle(raw_input: String, session_id: String, utility: Bool) -> String {
+    // Safety-screen history amplification now reads the SAME window the turn will be
+    // recorded into, so a session's own escalation pattern is what gets scored.
+    let history: String = state_get(conv_hist_key(session_id))
 
     // L1 in: safety screen
     let screen_result: String = safety_screen(raw_input, history)
@@ -423,8 +437,10 @@ fn layered_cycle(raw_input: String) -> String {
     let cont_action: String = json_get(continuity, "action")
 
     // Store continuity status so imprint can adjust its response register.
-    // TODO(reliability #4): session_continuity is process-global; scope per session_id
-    // when available to prevent cross-session bleed under concurrent layered_cycle calls.
+    // TODO(reliability #4) CLOSED 2026-08-05: this line was already written to scope per
+    // session — it just never received a session id, because the only source was a state key
+    // nothing wrote. It is now threaded from the route, so named sessions genuinely get their
+    // own continuity state and only anonymous callers share the global one.
     let cont_key: String = if str_eq(session_id, "") { "session_continuity" } else { "session_continuity:" + session_id }
     state_set(cont_key, cont_status)
 
@@ -453,40 +469,24 @@ fn layered_cycle(raw_input: String) -> String {
     let lc_aff_cutoff: Int = time_now() - 259200
     let lc_bell_nodes: String = engram_search_json("bell:soft bell:hard BellEvent affective", 2)
     let lc_has_bell: Bool = !str_eq(lc_bell_nodes, "") && !str_eq(lc_bell_nodes, "[]")
+    // CRASH FIX 2026-08-05 (BUG-PLAINCHAT-1): the " | ts:" parser used to be inline here.
+    // Inside this block-expression initializer elc compiled `lbmp + str_len(lbm)` to
+    // el_str_concat() on two integers, which segfaulted the whole daemon the moment a
+    // distress turn followed an earlier affective turn — i.e. exactly on the crisis path.
+    // Verified against the unmodified baseline binary AND present in the committed
+    // dist/soul.c. affective_node_ts() is a top-level function, where the same expression
+    // compiles to integer addition. Do not inline it back.
     let lc_bell_note: String = if lc_has_bell {
         let lb0: String = json_array_get(lc_bell_nodes, 0)
-        let lb_c: String = json_get(lb0, "content")
-        let lbm: String = " | ts:"
-        let lbmp: Int = str_index_of(lb_c, lbm)
-        let lb_ts_raw: String = if lbmp >= 0 {
-            let lbs: Int = lbmp + str_len(lbm)
-            let lbr: String = str_slice(lb_c, lbs, str_len(lb_c))
-            let lbn: Int = str_index_of(lbr, " | ")
-            if lbn < 0 { lbr } else { str_slice(lbr, 0, lbn) }
-        } else {
-            let lbca: String = json_get(lb0, "created_at")
-            if str_eq(lbca, "") { json_get(lb0, "updated_at") } else { lbca }
-        }
-        let lb_ts: Int = if str_eq(lb_ts_raw, "") { 0 } else { str_to_int(lb_ts_raw) }
+        let lb_ts: Int = affective_node_ts(lb0)
         if lb_ts > lc_aff_cutoff { "[AFFECTIVE NOTE: User was in distress in a recent session.]" } else { "" }
     } else { "" }
     let lc_pos_nodes: String = engram_search_json("PositiveEvent joy:high joy:low affective", 2)
     let lc_has_pos: Bool = !str_eq(lc_pos_nodes, "") && !str_eq(lc_pos_nodes, "[]")
+    // Same crash fix as the bell note above (BUG-PLAINCHAT-1).
     let lc_pos_note: String = if lc_has_pos && str_eq(lc_bell_note, "") {
         let lp0: String = json_array_get(lc_pos_nodes, 0)
-        let lp_c: String = json_get(lp0, "content")
-        let lpm: String = " | ts:"
-        let lpmp: Int = str_index_of(lp_c, lpm)
-        let lp_ts_raw: String = if lpmp >= 0 {
-            let lps: Int = lpmp + str_len(lpm)
-            let lpr: String = str_slice(lp_c, lps, str_len(lp_c))
-            let lpn: Int = str_index_of(lpr, " | ")
-            if lpn < 0 { lpr } else { str_slice(lpr, 0, lpn) }
-        } else {
-            let lpca: String = json_get(lp0, "created_at")
-            if str_eq(lpca, "") { json_get(lp0, "updated_at") } else { lpca }
-        }
-        let lp_ts: Int = if str_eq(lp_ts_raw, "") { 0 } else { str_to_int(lp_ts_raw) }
+        let lp_ts: Int = affective_node_ts(lp0)
         if lp_ts > lc_aff_cutoff { "[AFFECTIVE NOTE: User shared positive news in a recent session.]" } else { "" }
     } else { "" }
     let lc_affective_note: String = if !str_eq(lc_bell_note, "") { lc_bell_note } else { lc_pos_note }
@@ -498,11 +498,47 @@ fn layered_cycle(raw_input: String) -> String {
     }
     state_set("layered_cycle_safety_system_addendum", augmented_addendum)
 
-    // L3: imprint responds
-    let output: String = imprint_respond(aligned, imprint_id)
+    // L3: imprint responds — applies the active imprint's voice/domain annotation to the
+    // steward-aligned input. This produces the PROMPT, not the answer.
+    let prompt: String = imprint_respond(aligned, imprint_id)
 
-    // L1 out: validate output before delivery
-    return safety_validate(output, screen_action)
+    // L3b: the imprint SPEAKS (added 2026-08-05).
+    //
+    // Until now the cycle stopped at the annotation above, so /api/chat with agentic:false
+    // handed the user's own screened text back as the "reply" — every gate ran, but nothing
+    // ever generated. The generation is placed HERE, inside the cycle, rather than by
+    // pointing the route at handle_chat(): handle_chat has no enforcing input gate and no
+    // enforcing output gate, so calling it instead of this cycle would have traded the whole
+    // safety pipeline for a working reply. Composing keeps both.
+    //
+    // Order is deliberate and must not be rearranged: this call sits strictly AFTER the L1
+    // screen, the safe-mode guard, the hard-bell short-circuit and the L2 stewardship layers,
+    // and strictly BEFORE the L1 output gate. A hard bell never reaches a model — the branch
+    // above returns first. Tools are not offered on this turn; see layered_generate.
+    let output: String = layered_generate(prompt, imprint_id, session_id)
+
+    // L1 out: validate output before delivery. Still the terminal gate — nothing below this
+    // line can change the string this function returns.
+    let validated: String = safety_validate(output, screen_action)
+
+    // Turn bookkeeping. Records the VALIDATED text, never the raw model output, and is only
+    // reachable on the non-bell path: both bell branches above return before this point, so
+    // bell turns still never enter conversation history. Pure state side effect — it cannot
+    // alter what is returned.
+    //
+    // FIX A: the receipt is unconditional and always negative on this path, because on this
+    // path it is structurally true — layered_generate offers no tools at all (build_system_prompt
+    // chat mode + a request body with no "tools" key). Recording "no tools ran" is not padding:
+    // it is the only thing that distinguishes "nothing ran" from "we forgot to write down what
+    // ran", and that ambiguity is what made the model confess to a search it had performed.
+    //
+    // FIX E1: a utility generation is answered but not recorded. Guarded here rather than at
+    // the route so every /api/chat dispatch site inherits it from one place.
+    let receipt: String = tool_receipt("", "")
+    if !utility {
+        conv_history_record(session_id, raw_input, validated, receipt)
+    }
+    return validated
 }
 
 let soul_cgi_id_raw: String = env("SOUL_CGI_ID")
@@ -521,7 +557,28 @@ let axon_raw: String = env("NEURON_API_URL")
 let axon_base: String = if str_eq(axon_raw, "") { "http://localhost:7771" } else { axon_raw }
 
 let studio_dir_raw: String = env("SOUL_STUDIO_DIR")
-let studio_dir: String = if str_eq(studio_dir_raw, "") { "/Users/will/Development/neuron-technologies/products/cgi-studio/el-daemon" } else { studio_dir_raw }
+let studio_dir: String = if str_eq(studio_dir_raw, "") { env("HOME") + "/Development/neuron-technologies/products/cgi-studio/el-daemon" } else { studio_dir_raw }
+
+// RESTORED 2026-08-09 — this producer was added 2026-05-02 in 601e0fe and deleted
+// by the awareness refactor b163fa6 a few days later. Nothing has written
+// soul_identity since, while FIVE sites in chat.el kept reading it:
+//   chat.el:737, 1745, 2620, 3425, 3480 — each doing state_get("soul_identity")
+// and splicing the result into the system prompt beside the voice, security and
+// capability rules. They have been splicing an EMPTY STRING for roughly three
+// months. The identity section of every chat turn was blank and nothing said so.
+//
+// Found by the #132 state-key gate, which reports a read with no producer as a
+// build error rather than a silence — the whole reason that gate exists.
+//
+// Restored verbatim rather than improved: this key is an env-configurable persona
+// LINE, which is NOT the same thing as soul_identity_context (the graph-derived
+// [INTELLECTUAL-DNA]/[VALUES]/[MEMORY-PHILOSOPHY] block written at soul.el:184).
+// Pointing these five reads at that block instead would have substituted different
+// content and called it a fix. Whether the chat system prompt should ALSO carry the
+// graph-derived block is a real question, and a separate one.
+let identity_raw: String = env("SOUL_IDENTITY")
+let soul_identity: String = if str_eq(identity_raw, "") { "You are " + soul_cgi_id + ", a CGI." } else { identity_raw }
+state_set("soul_identity", soul_identity)
 
 println("[soul] boot - cgi=" + soul_cgi_id + " port=" + int_to_str(port))
 
@@ -621,6 +678,23 @@ if is_genesis && safe_to_seed {
     }
 }
 
+// CRASH RECOVERY (neuron#117). Deltas the previous process staged but could not
+// hand to the owner are still on disk — the spool is a filesystem queue, not a
+// memory buffer, precisely so that a soul that died mid-flight does not take its
+// unpushed writes with it. Drain them before serving, so recovered memories are
+// durable and recallable from the owner from the first request onward.
+//
+// Safe on a clean boot: an empty spool means no HTTP call at all. Safe in file
+// mode: wt_drain returns immediately when ENGRAM_URL is unset.
+let wt_recovered: Int = wt_drain()
+if wt_recovered > 0 {
+    println("[soul] write-through: recovered " + int_to_str(wt_recovered)
+        + " nodes from a previous process's spool -> persistence owner")
+}
+if wt_recovered < 0 {
+    println("[soul] write-through: spool present but the persistence owner is unreachable — queued, will retry on heartbeat")
+}
+
 println("[soul] serving on port " + int_to_str(port))
 http_serve_async(port, "handle_request")
 println("[soul] awareness loop starting")

soul.elh

@@ -1,6 +1,8 @@
 // auto-generated by elc --emit-header - do not edit
 extern fn init_soul_edges() -> Void
+extern fn ensure_self_canonical_bridge() -> Void
+extern fn aff_try_slot(slot_json: String, aff_7d_ts: Int, acc_key: String) -> Void
 extern fn load_identity_context() -> Void
 extern fn seed_persona_from_env() -> Void
 extern fn emit_session_start_event() -> Void
-extern fn layered_cycle(raw_input: String) -> String
+extern fn layered_cycle(raw_input: String, session_id: String, utility: Bool) -> String

stewardship.el

@@ -11,7 +11,7 @@ import "memory.el"
 fn steward_log_event(kind: String, detail: String) -> Void {
     let content: String = "STEWARD:" + kind + " | " + detail
     let tags: String = "[\"stewardship\",\"steward:" + kind + "\"]"
-    let discard: String = engram_node_full(
+    let discard: String = wt_node(
         content,
         "StewardshipEvent",
         "steward:" + kind,
@@ -221,7 +221,7 @@ fn steward_fingerprint_session(input: String, session_id: String) -> String {
         + " formality=" + fs_str
         + " time=" + tb_str
     let sample_tags: String = "[\"behavior\",\"BehaviorSample\",\"stewardship\"]"
-    let discard: String = engram_node_full(
+    let discard: String = wt_node(
         sample_content,
         "BehaviorSample",
         "behavior:" + session_id,

studio.el

@@ -53,8 +53,23 @@ fn handle_config(method: String, body: String) -> String {
 }
 
 fn dharma_registry() -> String {
+    // COMPILED IDENTITY, not state (2026-08-09). soul_principal had no producer at
+    // all — the #132 gate flagged it as a dead read and the registry reported an
+    // empty principal under a heading that says "Principal Covenant v1". The value
+    // was never missing: it is declared in soul.el's cgi block, and as of the
+    // codegen fix it is compiled into the binary and loaded at startup.
+    //
+    // Read it from the compiled constant rather than the state store. The design is
+    // explicit that this identity is "not modifiable by any runtime mechanism
+    // including environment variables, configuration files, or API calls" — so
+    // publishing it into state (the cheap fix) would have recreated exactly the
+    // mutable copy it forbids. cgi_principal() is read-only and has no setter.
+    //
+    // cgi_id keeps its state read deliberately: the RUNTIME instance id is a
+    // different fact from the compiled dharma_id, and conflating them would hide
+    // the case where a binary runs under an id its declaration never claimed.
     let cgi_id: String = state_get("soul_cgi_id")
-    let principal: String = state_get("soul_principal")
+    let principal: String = cgi_principal()
     return "{\"registry\":[{\"cgi\":\"" + cgi_id + "\","
         + "\"principal\":\"" + principal + "\","
         + "\"covenant\":\"Principal Covenant v1\","

tests/test_history_amplification.el

@@ -0,0 +1,213 @@
+// ── test_history_amplification.el ─────────────────────────────────────────────
+//
+// REGRESSION TEST FOR ISSUE #129 (P0, SAFETY).
+//
+// What this guards: on the agentic path, the crisis score has two halves — the
+// message you just sent, and the distress that has accumulated across the
+// conversation. The second half is the whole reason the escalation logic exists:
+// someone whose distress builds over several turns never sends one message that
+// trips the bell on its own.
+//
+// The defect this test was written against (ff421d3, 2026-08-05 → fixed
+// 2026-08-07): conversation history moved to a per-session key via
+// conv_hist_key(session_id), but the agentic path's safety screen was left
+// reading the old anonymous "conv_history" bucket. The desktop app always sends
+// a session_id, so the screen received "" on every real conversation and the
+// escalation half always scored 0. Nothing failed. Nothing logged. The comment
+// above the defective line documented this same bug being fixed once before.
+//
+// THE INVARIANT UNDER TEST, stated so it survives future renames:
+//   the window the safety screen READS must be the window conv_history_record
+//   WRITES. Not "must be called conv_history" — must AGREE.
+//
+// This test is deliberately written to fail loudly on the pre-fix source. If it
+// ever passes on code where the screen reads a key nothing writes, it is broken.
+//
+// To run (macOS, from the worktree root):
+//   scripts/run-el-test.sh tests/test_history_amplification.el
+// ──────────────────────────────────────────────────────────────────────────────
+
+import "../chat.el"
+import "../safety.el"
+import "../sessions.el"
+
+// Program class. Without this an El program compiles as a 'utility', and a
+// utility may not call the self-formation primitives (llm_call_system,
+// llm_vision) that chat.el's agentic loop references — the unit fails to
+// compile with a capability violation even though the test never calls them.
+// Declaring 'cgi' matches how soul.el declares itself.
+//
+// The endpoints below are deliberately DEAD: this test must never reach a live
+// engram, and nothing it asserts depends on one. Port 9 is discard.
+cgi "neuron-test-history-amplification" {
+    dharma_id: "ntn-test@http://127.0.0.1:9",
+    principal: "test-harness",
+    network:   "dharma-testnet",
+    engram:    "http://127.0.0.1:9"
+}
+
+// ── Counters ──────────────────────────────────────────────────────────────────
+//
+// NOTE for anyone copying this harness: the idiom used by the older tests in
+// this directory — `let pass_count = pass_count + 1` inside an assert function —
+// does NOT mutate the module-level binding. It declares a new local that dies
+// with the call, so those suites all print "0 passed, 0 failed" no matter what
+// happened. Counters go through the state store here so the summary is real.
+
+fn bump(counter: String) -> Void {
+    let cur: String = state_get(counter)
+    let n: Int = if str_eq(cur, "") { 0 } else { str_to_int(cur) }
+    state_set(counter, int_to_str(n + 1))
+}
+
+fn counter_of(counter: String) -> Int {
+    let cur: String = state_get(counter)
+    if str_eq(cur, "") { return 0 }
+    return str_to_int(cur)
+}
+
+fn assert_eq(label: String, got: String, expected: String) -> Void {
+    if str_eq(got, expected) {
+        bump("t_pass")
+        println("  PASS: " + label)
+    } else {
+        bump("t_fail")
+        println("  FAIL: " + label)
+        println("    got:      " + got)
+        println("    expected: " + expected)
+    }
+}
+
+fn assert_true(label: String, cond: Bool) -> Void {
+    if cond {
+        bump("t_pass")
+        println("  PASS: " + label)
+    } else {
+        bump("t_fail")
+        println("  FAIL: " + label)
+    }
+}
+
+// ── Fixtures ──────────────────────────────────────────────────────────────────
+//
+// ESCALATION_MSG scores 50 on its own ("can't go on", safety_score_crisis s9).
+// 50 is >= soft (35) and < hard (70): a soft bell by itself, which is the point.
+// It is the message that is only a crisis IN CONTEXT.
+//
+// DISTRESS_TURN carries five history phrases:
+//   hopeless 15 + worthless 15 + nobody cares 15 + can't take it anymore 20
+//   + want to disappear 20 = 85; contributed at 1/3 weight = 28.
+// 50 + 28 = 78 >= 70 → hard_bell. That 28-point swing IS the escalation logic,
+// and it is exactly what the defect suppressed.
+
+let TEST_SESSION: String = "sess-test-129-history-amplification"
+let ESCALATION_MSG: String = "honestly i can't go on like this"
+let DISTRESS_TURN: String = "i feel hopeless and worthless, nobody cares, i can't take it anymore, i want to disappear"
+
+println("")
+println("test_history_amplification.el — issue #129 (agentic multi-turn crisis escalation)")
+
+// ── 1. Baseline: the message alone is a SOFT bell, not a hard one ─────────────
+//
+// If this ever returns hard_bell, the test below proves nothing — the message
+// would trip the bell without any history and the amplification would be
+// invisible. This assertion is what keeps the real test honest.
+
+println("")
+println("1. baseline — escalation message with NO history is a soft bell")
+
+let baseline: String = safety_screen(ESCALATION_MSG, "")
+assert_eq("no history -> soft_bell (not hard)", json_get(baseline, "action"), "soft_bell")
+
+// ── 2. Producer sanity: history lands in the session's own window ─────────────
+
+println("")
+println("2. producer — conv_history_record writes the session's window")
+
+conv_history_record(TEST_SESSION, DISTRESS_TURN, "i hear you, that sounds heavy", "")
+
+let written: String = state_get(conv_hist_key(TEST_SESSION))
+assert_true("session window is non-empty after record", !str_eq(written, ""))
+assert_true("session window contains the distress turn", str_contains(written, "hopeless"))
+
+// ── 3. THE REGRESSION: the agentic screen must SEE that window ────────────────
+//
+// Pre-fix this returns soft_bell, because agentic_safety_screen read the
+// anonymous bucket and got "". Post-fix it returns hard_bell.
+
+println("")
+println("3. REGRESSION #129 — agentic screen reads the session's own window")
+
+let screened: String = agentic_safety_screen(TEST_SESSION, ESCALATION_MSG)
+assert_eq(
+    "distress history escalates the agentic screen to hard_bell",
+    json_get(screened, "action"),
+    "hard_bell"
+)
+
+// ── 4. The invariant, stated directly ─────────────────────────────────────────
+//
+// Independent of thresholds and phrase lists: whatever the screen reads for a
+// session must equal what the recorder wrote for that session. This is the
+// assertion that survives a future rename of either side.
+
+println("")
+println("4. invariant — read window == written window")
+
+let read_back: String = state_get(conv_hist_key(TEST_SESSION))
+assert_true("screen input is the recorded window, not empty", !str_eq(read_back, ""))
+assert_eq("read window is byte-identical to written window", read_back, written)
+
+// ── 5. No false positive: a calm session does not escalate ────────────────────
+//
+// A test that only ever asserts "hard_bell" would pass on code that hard-bells
+// every message. This is the other leg, and it runs BEFORE the anonymous case
+// below on purpose: that case writes the shared bucket, and under the defect a
+// calm session would then inherit it.
+
+println("")
+println("5. specificity — a calm history does NOT escalate")
+
+let CALM_SESSION: String = "sess-test-129-calm"
+state_set("conv_history", "")
+conv_history_record(CALM_SESSION, "what is the weather like today", "clear and mild", "")
+let calm: String = agentic_safety_screen(CALM_SESSION, ESCALATION_MSG)
+assert_eq("calm history stays at soft_bell", json_get(calm, "action"), "soft_bell")
+
+// ── 6. Cross-session leakage ──────────────────────────────────────────────────
+//
+// The same defect had a second face: because the screen read one shared bucket,
+// a calm session could be scored against a DIFFERENT session's distress. That is
+// wrong in both directions — it fabricates a crisis for the calm user and it
+// leaks the distressed user's content into another session's scoring.
+
+println("")
+println("6. isolation — one session's distress must not score another session")
+
+state_set("conv_history", "")
+let OTHER_SESSION: String = "sess-test-129-other"
+conv_history_record(OTHER_SESSION, DISTRESS_TURN, "i hear you", "")
+let isolated: String = agentic_safety_screen(CALM_SESSION, ESCALATION_MSG)
+assert_eq(
+    "a distressed OTHER session does not escalate the calm session",
+    json_get(isolated, "action"),
+    "soft_bell"
+)
+
+// ── 7. Anonymous sessions still work ──────────────────────────────────────────
+//
+// conv_hist_key("") deliberately falls back to the shared "conv_history" bucket.
+// The fix must not break the no-session_id path older callers rely on. Runs last
+// because it writes that shared bucket.
+
+println("")
+println("7. anonymous path — empty session_id still screens against the shared window")
+
+state_set("conv_history", "[{\"role\":\"user\",\"content\":\"" + DISTRESS_TURN + "\"}]")
+let anon: String = agentic_safety_screen("", ESCALATION_MSG)
+assert_eq("anonymous session escalates too", json_get(anon, "action"), "hard_bell")
+
+// ── Summary ───────────────────────────────────────────────────────────────────
+
+println("")
+println("history amplification tests: " + int_to_str(counter_of("t_pass")) + " passed, " + int_to_str(counter_of("t_fail")) + " failed")

tools/build-soul-from-dist.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+# build-soul-from-dist.sh — build a deployable soul from the SAME input CI compiles.
+#
+# THE PROBLEM THIS CLOSES: until now, deploys were built by build-soul.sh, which
+# compiles a scratch amalgam and never touches dist/soul.c. CI compiles dist/soul.c.
+# Two lineages. On 2026-08-09 the committed input fell 2,761 bytes behind the sources
+# while three binaries built the other way were installed on the operator machine —
+# so "what runs" and "what the repo says builds" were different artifacts again,
+# which is the whole of #133 and #111 wearing new clothes.
+#
+# This builds from dist/soul.c with CI's own flags, after asserting that dist/soul.c
+# actually matches the .el sources, and writes a provenance sidecar so a deployer can
+# refuse anything of unknown origin.
+#
+# -rdynamic and -DHAVE_CURL are copied from .gitea/workflows/ci.yaml deliberately.
+# The CI comment explains -rdynamic: without it the runtime cannot resolve its HTTP
+# handler by name via dlsym and the binary serves nothing on every route.
+#
+# usage: build-soul-from-dist.sh <out-binary>
+set -u
+OUT="${1:?usage: build-soul-from-dist.sh <out-binary>}"
+ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+RUNTIME="$ROOT/vendor/el-runtime/v1.0.0-20260501"
+
+cd "$ROOT" || exit 2
+
+echo "[build-from-dist] GATE: does dist/soul.c match the sources?"
+if ! ./tools/soulc-stamp.sh --check; then
+  echo "[build-from-dist] REFUSING — the build input is stale. Regenerate and stamp first." >&2
+  exit 9
+fi
+
+[ -f "$RUNTIME/el_runtime.c" ] || { echo "pinned runtime missing at $RUNTIME" >&2; exit 2; }
+
+echo "[build-from-dist] compiling dist/soul.c with CI's flags"
+cc -O2 -DHAVE_CURL -rdynamic \
+  -I"$RUNTIME" \
+  dist/soul.c \
+  "$RUNTIME/el_runtime.c" \
+  -lcurl -lpthread -lm \
+  -o "$OUT" || { echo "[build-from-dist] COMPILE FAILED" >&2; exit 3; }
+
+# Provenance sidecar: what a deployer checks before installing anything.
+SRC_SHA="$(shasum -a 256 dist/soul.c | awk '{print $1}')"
+STAMP_SHA="$(shasum -a 256 dist/soul.c.stamp | awk '{print $1}')"
+COMMIT="$(git rev-parse HEAD 2>/dev/null || echo unknown)"
+DIRTY="clean"; [ -n "$(git status --porcelain -- '*.el' dist/soul.c 2>/dev/null)" ] && DIRTY="DIRTY"
+cat > "$OUT.provenance" <<EOF
+{"built_from":"dist/soul.c",
+ "dist_soul_c_sha256":"$SRC_SHA",
+ "stamp_sha256":"$STAMP_SHA",
+ "git_commit":"$COMMIT",
+ "worktree":"$DIRTY",
+ "runtime":"vendor/el-runtime/v1.0.0-20260501",
+ "flags":"-O2 -DHAVE_CURL -rdynamic"}
+EOF
+
+echo "[build-from-dist] OK -> $OUT ($(wc -c < "$OUT" | tr -d ' ') bytes)"
+echo "[build-from-dist] provenance -> $OUT.provenance (commit ${COMMIT:0:8}, worktree $DIRTY)"

tools/retrieval-eval/README.md

@@ -0,0 +1,147 @@
+# Retrieval eval harness
+
+Measures Neuron's memory retrieval so a change can be shown to help before it is
+believed to help. Nothing else on the memory roadmap should ship without a run
+through this.
+
+```
+tools/retrieval-eval/run_comparison.sh --baseline main --candidate <branch>
+```
+
+That builds a soul from each ref, boots each in isolation on a fixed corpus,
+runs the gold set three times per ref, and prints a table plus a verdict that
+refuses to call a difference real if it is inside the noise band.
+
+## What was reused
+
+This is not a new idea, it is the missing third of an existing one.
+
+| Prior work | What it gave | What was missing |
+|---|---|---|
+| `docs/research/graphrag_eval/` (`collect.py`, `score.py`, 2026-06-08) | The three-retriever comparison that produced the numbers everyone quotes: substring 1.7% P@5, graph 21.7%, BM25 55%. Per-query relevant-id scoring, fixed-denominator precision@5, unique-relevant analysis. | 13 hand-written queries, judged by an LLM after the fact; measured the *live* soul on the *live* engram. |
+| `docs/research-archive/p0-prototypes/eval_pinned_40q_20260715.py` | The pinned-query discipline: ground truth committed as regexes so every run judges alike, plus a `--check` winnability gate. 40 queries in 5 bands including a deliberate paraphrase-hard band. | Scored offline replicas of substring/BM25 — it never ran the real retrieval path. |
+| `docs/research-archive/p0-prototypes/stage0_eval_20260714.py` | The `hit@5` metric and the substring/BM25 reference implementations. | Same: offline only. |
+| `scripts/verify-soul-contract.sh` | The isolation recipe, verbatim: throwaway port, throwaway `HOME`, `SOUL_ENGRAM_PATH`, and the non-obvious `SOUL_ISE_URL` pin that stops an "isolated" soul silently syncing the operator's live brain. | It is a contract gate, not a measurement. |
+| `_engine-liveness-91/gen-soul-amalgam.sh` + `.gitea/workflows/ci.yaml` | The build recipe (`elc --target=c` with every `.elh` on the import chain removed) and CI's exact compile flags. | — |
+
+**Reused directly:** the isolation recipe, the build recipe, fixed-denominator
+precision@5, the pinned-ground-truth and winnability ideas.
+**New here:** ids rather than regexes as ground truth, an associative category
+derived from real graph edges, a superseded/contradicted category scored on
+ranking, a machine-checked zero-lexical-overlap guarantee on paraphrases,
+paired significance testing, and — the point — measurement against the **real
+compiled soul** rather than an offline replica of one leg of it.
+
+## Design fit
+
+The thing under measurement is Will's designed retrieval: spreading activation
+over the weighted directed graph, four-factor multiplicative scoring (parent
+strength x edge weight x target salience x query/target cosine). A Python
+re-implementation would measure my reading of the design. So the harness
+compiles the actual `soul.el` amalgam and asks it over HTTP on
+`/api/neuron/recall`, exactly as the MCP wrapper and the app do.
+
+## Files
+
+| File | Does |
+|---|---|
+| `build_gold_set.py` | Derives and **validates** the gold set from the corpus. `--check` re-validates and exits non-zero if a query became unwinnable or a paraphrase leaked a word. |
+| `gold_set.json` | 38 queries. Every one carries a `derivation` string. |
+| `run_eval.py` | Boots one soul in isolation, runs the gold set, writes metrics. Kills and **confirms dead** its child; records the confirmation in the results file. |
+| `compare.py` | Paired diff of two result files with McNemar's exact test and a stated noise floor. |
+| `build-soul.sh` | Compiles a soul binary from a plain source tree. |
+| `run_comparison.sh` | All of the above, end to end, from two git refs. |
+
+## The gold set — 38 queries
+
+Built from the real corpus (`snapshot-pre-repair-20260806.json`, 78,768 nodes /
+14,214 edges) so it reflects one person's accumulating memory, not document QA.
+
+| Category | n | Expected answer derived by |
+|---|---|---|
+| `exact_rare` | 6 | **Mined.** Tokens with document frequency 1 across all 78,768 nodes, whose single containing node is a 300–6000 char Memory/Knowledge/Belief. That node is the only possible answer. Re-verified every build. |
+| `phrase` | 7 | **Mined.** Case-insensitive verbatim scan; the matching set *is* the answer key. Phrases matching >25 nodes are rejected as too diffuse. |
+| `paraphrase` | 13 | **Hand-selected, machine-checked.** Target locked by id; the build then proves that **zero** content words of the query appear anywhere in the target's label, content, or tags. A leak fails the build — the category cannot quietly decay into lexical matching. |
+| `associative` | 6 | **Derived from edges.** Query built from one value node's distinctive vocabulary; expected answers are its siblings on the `Self - Values (grounded)` hub. Siblings sharing any query word are dropped, so the only route from query to answer is seed -> hub -> sibling. |
+| `nonsense` | 3 | **Control.** Verified that no token occurs anywhere in the corpus. Correct behaviour is to return nothing. |
+| `superseded` | 3 | **Derived.** Correction/stale pairs located by regex scan, kept only when both sides resolve to different surviving nodes. Scored on **ranking**: the correction must be returned *and* rank above the stale node. |
+
+## Metrics
+
+`hit@5`, `recall@5`, `recall@10`, `precision@5` (fixed denominator 5, so an
+empty result is punished like a page of junk), `MRR@10`, and wall-clock latency
+per query (p50/p95/max). Output is a table plus a machine-readable JSON per run
+so runs can be diffed.
+
+## Honesty about noise
+
+- **Minimum detectable swing on this 38-query set: 6 queries.** If every query
+  that changes changes the same way, `p = 2 x 0.5^n`, which first drops under
+  0.05 at n=6. Any net change smaller than that is inside the noise band and
+  `compare.py` says so in those words.
+- **Run-to-run drift is measured, not assumed.** Activation is a stateful read
+  by design (traversal reinforces what it touches), so identical inputs need not
+  give identical outputs. Observed: `main` 0 queries of drift across 3 runs
+  (fully deterministic); the activation branch 1 query.
+- The noise floor used for the verdict is `max(6, observed_drift + 1)`.
+- **This gold set is underpowered for small effects.** A genuine 3-query
+  improvement would not clear the bar. Growing the set is the fix; until then, a
+  small positive delta means "not shown", not "no effect".
+
+## First result: `main` vs `feat/recall-through-activation`
+
+Corpus and gold set identical, three runs each, fresh corpus copy per run.
+
+| | main | recall-through-activation | delta |
+|---|---|---|---|
+| hit@5 | 34.3% | 22.9% | **-11.4pp** |
+| recall@5 | 26.9% | 19.1% | -7.9pp |
+| recall@10 | 33.3% | 24.3% | -9.1pp |
+| precision@5 | 12.0% | 7.4% | -4.6pp |
+| MRR@10 | 0.294 | 0.242 | -0.053 |
+| latency p50 | 1140 ms | 3209 ms | **2.81x** |
+| latency p95 | 1584 ms | 4852 ms | 3.06x |
+| nonsense clean | 2/3 | 2/3 | — |
+| superseded outranks | 1/3 | 0/3 | -1 |
+
+By category (hit@5):
+
+| category | main | activation |
+|---|---|---|
+| exact_rare | 100% | 100% |
+| phrase | 85.7% | **28.6%** |
+| paraphrase | 0% | 0% |
+| associative | 0% | 0% |
+| superseded | 0% | 0% |
+
+**Verdict: directionally worse, one query short of significant.** 5 discordant
+pairs, all 5 against the candidate, 0 for it. McNemar exact p = 0.0625 — under
+the stated rule that is *inside* the noise band, so the harness reports "no
+measurable difference" on accuracy and the honest summary is "5 for 5 the wrong
+way, needs a 6th or a larger gold set to call".
+
+Latency is a different story: 2.8x at p50 is deterministic and far outside any
+noise band. That regression is real.
+
+The result the branch was written for did not appear. Its stated purpose was to
+recover sibling nodes one hub-hop away — the `associative` category — and that
+category is **0/6 on both builds**. Probing directly: for the query
+`Marines hernia sepsis medical ward`, the activation build returns the lexical
+seed node itself at rank 8, and none of its 12 hub siblings anywhere in the top
+10. The traversal is running; it is not reaching siblings.
+
+Two corpus facts likely explain it, and both are measurable rather than
+speculative:
+
+1. **The graph is nearly edgeless.** Only 4,060 of 78,768 nodes (5.2%) carry any
+   edge at all — 14,214 edges total, 0.18 per node. Spreading activation over a
+   graph with no edges is an expensive way to do lexical matching, which is
+   roughly what the numbers show.
+2. **No embeddings.** No node in this snapshot has an embedding field, so the
+   fourth factor of the four-factor product — query/target cosine similarity —
+   has nothing to compute from, and the semantic seeding pass is inert.
+
+That is the harness earning its keep on its first job: the change would have
+felt like progress (it is the designed mechanism, and it does run) and measures
+as a regression on phrase queries plus a 2.8x latency cost, with its intended
+benefit unrealised because the corpus lacks the structure it needs.

tools/retrieval-eval/bestval.py

@@ -0,0 +1,21 @@
+import numpy as np, json, urllib.request
+SP="/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad"
+np.seterr(all='ignore')
+M=np.load(SP+'/emb.npy'); eids=open(SP+'/ids.txt',encoding='utf-8',errors='surrogateescape').read().split('\n')
+eidx={k:i for i,k in enumerate(eids)}
+gold=json.load(open("/Users/timlingo/Development/neuron-technologies/_wt-assoc-leg/tools/retrieval-eval/gold_set.json"))['queries']
+VALS=sorted({r for q in gold if q['category']=='paraphrase' for r in q['relevant']})
+VI=[eidx[v] for v in VALS]
+def emb(t):
+    b=json.dumps({"model":"nomic-embed-text","prompt":t}).encode()
+    r=urllib.request.Request("http://127.0.0.1:11434/api/embeddings",data=b,headers={"Content-Type":"application/json"})
+    v=np.array(json.load(urllib.request.urlopen(r,timeout=60))["embedding"],dtype=np.float32)
+    return v/(np.linalg.norm(v)+1e-9)
+print("qid  cat         bestValueNodeGlobalRank   goldGlobalRank  goldSiblingRank")
+for q in gold:
+    if q['category']!='paraphrase': continue
+    v=emb(q['query']); s=M@v; s[~np.isfinite(s)]=-1
+    ranks=sorted(int((s>s[j]).sum())+1 for j in VI)
+    g=eidx[q['relevant'][0]]; gr=int((s>s[g]).sum())+1
+    sv=np.array([s[j] for j in VI]); sib=int((sv>s[g]).sum())+1
+    print("%-4s %-11s best=%-5d (top3 val ranks %s)  gold=%-5d sib=%d" % (q['id'],q['category'],ranks[0],ranks[:3],gr,sib))

tools/retrieval-eval/build-soul.sh

@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+# build-soul.sh — compile a soul binary from a plain source tree (no git needed).
+#
+# Reuses the amalgam recipe worked out in gen-soul-amalgam.sh (round 9.1) and the
+# compile flags from .gitea/workflows/ci.yaml, so the binary under test is the
+# same translation unit CI ships — not a re-implementation.
+#
+#   elc --target=c emits only an extern prototype for any module that has a .elh
+#   header beside it, and inlines the module's bodies when it does not. So the
+#   amalgam is produced in a scratch copy with every .elh on the import chain
+#   deleted.
+#
+# usage: build-soul.sh <src-tree-with-*.el> <out-binary>
+set -euo pipefail
+SRC="${1:?usage: build-soul.sh <src-tree> <out-binary>}"
+OUT="${2:?out-binary}"
+ELC="${ELC:-$HOME/neuron-dev-stack/src/el/lang/dist/platform/elc}"
+EL_REPO="${EL_REPO:-$HOME/Development/neuron-technologies/el}"
+RTDIR="${RTDIR:-$SRC/vendor/el-runtime/v1.0.0-20260501}"
+SSL="${SSL_PREFIX:-/opt/homebrew/opt/openssl@3}"
+
+[ -x "$ELC" ] || { echo "no elc at $ELC" >&2; exit 2; }
+[ -f "$RTDIR/el_runtime.c" ] || { echo "no el_runtime.c at $RTDIR" >&2; exit 2; }
+
+GEN="$(mktemp -d "${TMPDIR:-/tmp}/soul-build.XXXXXX")"
+trap 'rm -rf "$GEN"' EXIT
+mkdir -p "$GEN/neuron" "$GEN/foundation/el/elp/src"
+cp "$SRC"/*.el "$GEN/neuron/"
+cp "$EL_REPO"/elp/src/*.el "$GEN/foundation/el/elp/src/"
+find "$GEN" -name '*.elh' -delete
+
+( cd "$GEN/neuron" && "$ELC" --target=c soul.el ) > "$GEN/soul.c"
+BODIES=$(grep -c '^el_val_t .*) {$' "$GEN/soul.c" || true)
+echo "[build-soul] amalgam $(wc -c < "$GEN/soul.c" | tr -d ' ') bytes, ${BODIES} inlined bodies"
+[ "$BODIES" -ge 1200 ] || { echo "[build-soul] FAIL: only $BODIES bodies — an import was not inlined"; exit 1; }
+
+cc -O2 -DHAVE_CURL -rdynamic \
+   -I"$RTDIR" -I"$SSL/include" -L"$SSL/lib" \
+   "$GEN/soul.c" "$RTDIR/el_runtime.c" \
+   -lssl -lcrypto -lcurl -lpthread -lm \
+   -o "$OUT" 2> "$GEN/cc.log" || { echo "[build-soul] FAIL compile"; tail -40 "$GEN/cc.log"; exit 1; }
+if grep -qE 'implicit.*(engram_|el_)' "$GEN/cc.log"; then
+  echo "[build-soul] FAIL: implicit declarations of runtime symbols"; grep -E 'implicit' "$GEN/cc.log" | head; exit 1; fi
+echo "[build-soul] OK -> $OUT ($(wc -c < "$OUT" | tr -d ' ') bytes)"

tools/retrieval-eval/build_gold_set.py

@@ -0,0 +1,506 @@
+#!/usr/bin/env python3
+"""
+build_gold_set.py — derive the retrieval gold set FROM the corpus, and validate it.
+
+WHY THIS FILE EXISTS AS CODE AND NOT AS A HAND-WRITTEN JSON
+    A gold set nobody can audit is vibes with extra steps. Every expected answer
+    here is either (a) mined from the corpus by a rule this script re-runs, or
+    (b) hand-selected with a stated criterion that this script then CHECKS
+    against the corpus. Both leave a `derivation` string on every query, and the
+    checks are re-run on demand so the set cannot silently rot as the corpus
+    changes.
+
+    Lineage: this extends the pinned-query approach from
+    docs/research-archive/p0-prototypes/eval_pinned_40q_20260715.py (pinned
+    ground-truth patterns + a --check "winnability" gate) and the per-query
+    relevant-id scoring from docs/research/graphrag_eval/score.py. What is new:
+    ids as ground truth rather than regexes alone, an ASSOCIATIVE category
+    derived from real graph edges, a superseded/contradicted category, and a
+    machine-checked no-lexical-overlap guarantee on the paraphrase category.
+
+THE SIX CATEGORIES, AND WHAT EACH ONE IS FOR
+    exact_rare   a single rare word. Substring matching already wins these.
+                 They are a REGRESSION GUARD: any change that loses them is
+                 disqualified regardless of what else it gains.
+    phrase       a multi-word string that exists verbatim in the corpus.
+                 Guards multi-token queries, which the old substring matcher
+                 handled by returning nothing.
+    paraphrase   same meaning, ZERO shared content words with the target node.
+                 THE CATEGORY THAT MATTERS. Mechanically unreachable by string
+                 matching; reachable only by semantics or by association.
+    associative  the answer is one hub-hop from an obvious starting point and
+                 shares no words with the query. This is the case the graph is
+                 supposed to buy: query one value, get its siblings.
+    nonsense     must return nothing. Guards against a retriever that "improves"
+                 recall by returning the whole graph.
+    superseded   a fact that was later corrected. The correction must OUTRANK
+                 the stale version — ranking, not mere presence.
+
+usage:
+    python3 build_gold_set.py <snapshot.json> [--out gold_set.json] [--check]
+    --check re-validates an existing gold_set.json against the corpus and exits
+    non-zero if any query became unwinnable or any paraphrase leaked a word.
+"""
+import argparse
+import json
+import os
+import re
+import sys
+from collections import Counter, defaultdict
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+DEFAULT_OUT = os.path.join(HERE, "gold_set.json")
+
+TOKEN = re.compile(r"[a-z0-9][a-z0-9\-']*")
+
+# Stopwords are deliberately generous. A paraphrase query is only interesting if
+# its CONTENT words are absent from the target; "the", "is", "what" appearing in
+# both proves nothing. Being generous here makes the overlap test STRICTER on
+# the words that carry meaning, which is the conservative direction.
+STOP = set("""
+a about above after again against all also am an and any are aren't as at be because been
+before being below between both but by can can't cannot could couldn't did didn't do does
+doesn't doing don't down during each few for from further had hadn't has hasn't have haven't
+having he her here hers herself him himself his how i if in into is isn't it its itself just
+me more most my myself no nor not of off on once only or other others ought our ours ourselves
+out over own same shan't she should shouldn't so some such than that the their theirs them
+themselves then there these they this those through to too under until up very was wasn't we
+were weren't what when where which while who whom why will with won't would wouldn't you your
+yours yourself yourselves get gets got make makes made take takes use uses used way ways thing
+things does doing done keep keeps kept go goes going come comes came one two something anything
+""".split())
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# corpus helpers
+# ─────────────────────────────────────────────────────────────────────────────
+def load_corpus(path):
+    with open(path, encoding="utf-8", errors="replace") as fh:
+        data = json.load(fh)
+    nodes = [n for n in data.get("nodes", []) if isinstance(n, dict) and n.get("id")]
+    edges = [e for e in data.get("edges", []) if isinstance(e, dict)]
+    return nodes, edges
+
+
+def doctext(n):
+    return " ".join([str(n.get("label") or ""), str(n.get("content") or ""), str(n.get("tags") or "")])
+
+
+def content_tokens(s):
+    return {t for t in TOKEN.findall(s.lower()) if t not in STOP and len(t) > 2}
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# hand-authored queries. Every entry states HOW its expected answer was chosen.
+# The `check` field names the validation this script runs against the corpus.
+# ─────────────────────────────────────────────────────────────────────────────
+
+# EXACT_RARE — mined, not chosen. The rule (re-run by mine_exact_rare below):
+# tokens whose document frequency across the whole corpus is 1, whose single
+# containing node is a Memory/Knowledge/Belief with 300-6000 chars of content
+# (so the answer is a real memory, not a 117KB whitepaper that contains every
+# word in English), and whose token is plain lowercase alphabetic. The expected
+# answer is that one node — it is the only node that can possibly be correct.
+EXACT_RARE_SEEDS = [
+    "unjailbreakable",
+    "engram-migrate",
+    "cartabandonedevent",
+    "pre-apprenticeship",
+    "inferencenodemanager",
+    "clear-eyed",
+]
+
+# PHRASE — chosen by reading the corpus for phrases that (a) occur verbatim,
+# (b) occur in a small enough set of nodes that "relevant" is well defined.
+# Expected answers are computed here as EVERY node whose text contains the
+# phrase case-insensitively — so the answer set is a fact about the corpus, not
+# an opinion. Queries whose phrase matches more than PHRASE_MAX nodes are
+# rejected by validation as too diffuse to score.
+PHRASE_MAX = 25
+PHRASE_SEEDS = [
+    ("patterns not returns",
+     "a verbatim correction Will issued; expected = every node containing the phrase"),
+    ("thirty moves",
+     "the canonical biographical phrase; expected = every node containing it"),
+    ("Grandma Lucas",
+     "a named person appearing verbatim in the biography/value nodes"),
+    ("Directed Harmonic",
+     "the canonical DHARMA expansion, confirmed by Will April 24 2026"),
+    ("Sarah Bishop",
+     "a named person; rare enough that the answer set is unambiguous"),
+    ("Directed Autonomous Runtime Modification",
+     "the DARMA expansion, quoted verbatim in the backlog item and its correction"),
+    ("zero-knowledge encrypted backup",
+     "the paid-tier feature name as written in the roadmap nodes"),
+]
+
+# PARAPHRASE — hand-authored. THE SELECTION CRITERION, stated once and applied
+# to all nine: pick a node whose SUBJECT is unmistakable to a reader, then write
+# the query a person would actually type when they remember the subject but not
+# the words. The target is then LOCKED by id, and this script enforces the hard
+# property that makes the category meaningful: not one content word of the query
+# appears anywhere in the target node's label, content, or tags. If a word
+# leaks, validation fails and the query must be rewritten — the set cannot
+# quietly degrade into a lexical query wearing a paraphrase costume.
+PARAPHRASE_SEEDS = [
+    ("kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+     "the elderly relative who passed while he stayed away",
+     "target: 'Value - Do the Essential Thing While You Can', whose subject is Grandma Lucas "
+     "dying in Feb 2006 without Will saying goodbye. Query names the event with none of the "
+     "node's own vocabulary."),
+    ("kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+     "a soldier sidelined by illness who refused to quit",
+     "target: 'Value - Survival Is Not an Excuse to Stop', whose subject is enlisting in the "
+     "Marines, a severe hernia, and sepsis. Query describes the episode obliquely."),
+    ("kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+     "choosing an uncomfortable fact over a pleasant fiction",
+     "target: 'Value - Honesty Before Comfort'. Query states the principle in wholly "
+     "different words."),
+    ("kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
+     "a tight payload beats a bloated one",
+     "target: 'Value - Precision Over Brute Force'. Query restates the claim with no "
+     "shared vocabulary."),
+    ("kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+     "if you are able and nobody is coming the job is yours",
+     "target: 'Value - Capability Is a Debt You Owe the Moment'. Query states the "
+     "obligation without the node's terms."),
+    ("kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+     "learning is the wealth creditors cannot seize",
+     "target: 'Value - Knowledge Survives When Nothing Else Does', whose subject is the "
+     "library following Will across 30+ moves."),
+    ("kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+     "reliability proven by track record not assertion",
+     "target: 'Value - Earned Trust' ('Trust is demonstrated, not declared')."),
+    ("kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+     "boundaries that enable instead of confine",
+     "target: 'Value - Constraints as Freedom'. Query is a restatement of the same claim."),
+    ("kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+     "what shifts tells you where to cut a system apart",
+     "target: 'Value - Change Is the Signal', the value VBD is built on."),
+    ("kn-f230b362-b201-4402-9833-4160c89ab3d4",
+     "a mind that compounds instead of resetting each day",
+     "target: 'Value - The System Must Accumulate'. Query is the accumulation claim in "
+     "different vocabulary."),
+    ("kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+     "loved for the unedited self and not the polished exterior",
+     "target: 'Value - Being Seen Is Rarer Than Being Known', whose subject is Sarah Bishop "
+     "as the first person Will did not perform for."),
+    ("kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+     "cheerfulness you arrive at instead of assuming",
+     "target: 'Value - Hope Is a Conclusion'. Query restates 'a conclusion, not a premise'."),
+    ("kn-6061318f-046b-4935-907d-8eafdce14930",
+     "a childhood offering no solid foundation to inherit",
+     "target: 'Value - Structure Is Not Inherited', whose subject is thirty moves between "
+     "two parents' collapses."),
+]
+
+# ASSOCIATIVE — derived from real edges, not authored. The construction:
+# every value node hangs off the 'Self - Values (grounded)' hub by an `identity`
+# edge. For a chosen value node V, the query is built from V's own distinctive
+# vocabulary; the expected answers are V's SIBLINGS on that hub. A sibling
+# shares no query words with the query by construction (validated below), so the
+# only path from the query to a sibling is: lexical seed on V -> hub -> sibling.
+# That is a two-hop traversal and nothing else can produce it.
+VALUES_HUB = "kn-5b606390-a52d-4ca2-8e0e-eba141d13440"
+ASSOCIATIVE_SEEDS = [
+    ("kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71", "Grandma Lucas stroke February 2006 goodbye window"),
+    ("kn-58874a74-b96f-4883-9e08-45707f4bd3ee", "Marines hernia sepsis medical ward"),
+    ("kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e", "Sarah Bishop Dyer trailer performance"),
+    ("kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83", "Swarm Architecture containment lateral worker"),
+    ("kn-e0423482-cfa5-4796-8689-8495c93b66bc", "hope won inside the narrative preface"),
+    ("kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8", "man of the house six years old expectation"),
+]
+
+# NONSENSE — must return nothing. Strings chosen to be lexically impossible:
+# validation asserts each appears in ZERO corpus nodes as a substring and that
+# none of its tokens appears anywhere either (so not even a partial seed exists).
+NONSENSE_SEEDS = [
+    "zqxjvw plimforth grebulon",
+    "flarnbistle quommetry",
+    "xxqzzt vurblenacht throom",
+]
+
+# SUPERSEDED — a fact that was corrected. Chosen by searching the corpus for
+# explicit correction language and keeping pairs where BOTH the stale statement
+# and its correction exist as separate nodes. Scored on RANKING: the correction
+# must appear, and must appear above the stale node. Ids are locked here and
+# validated to exist and to match their stated role.
+SUPERSEDED_SEEDS = [
+    # (query, correct_id, stale_id, derivation)
+]
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# mining
+# ─────────────────────────────────────────────────────────────────────────────
+def mine_exact_rare(nodes, byid, seeds):
+    """Re-derive: confirm each seed token still has df==1 and name its node."""
+    tok = re.compile(r"[A-Za-z][A-Za-z0-9\-]{4,}")
+    want = set(seeds)
+    df = Counter()
+    post = defaultdict(set)
+    for n in nodes:
+        for t in {w.lower() for w in tok.findall(doctext(n))}:
+            if t in want:
+                df[t] += 1
+                post[t].add(n["id"])
+    out = []
+    for s in seeds:
+        ids = sorted(post.get(s, ()))
+        out.append((s, ids, df.get(s, 0)))
+    return out
+
+
+def phrase_matches(nodes, phrase):
+    p = phrase.lower()
+    return sorted(n["id"] for n in nodes if p in doctext(n).lower())
+
+
+def hub_siblings(edges, hub, relation="identity"):
+    sibs = []
+    for e in edges:
+        if e.get("from_id") == hub and e.get("relation") == relation:
+            sibs.append(e["to_id"])
+        elif e.get("to_id") == hub and e.get("relation") == relation:
+            sibs.append(e["from_id"])
+    return list(dict.fromkeys(sibs))
+
+
+def find_superseded_pairs(nodes, byid):
+    """Locked pairs, each verified here to exist and to carry its stated marker.
+
+    Chosen by scanning the corpus for explicit correction language
+    (CORRECTION/SUPERSEDES/re-corrected/no longer/RECONCILED) and keeping only
+    cases where the STALE claim also survives as its own node — a supersession
+    with nothing to outrank is not a ranking test.
+    """
+    pairs = []
+    txt = {n["id"]: doctext(n) for n in nodes}
+
+    def find_one(pattern, exclude=()):
+        rx = re.compile(pattern)
+        return [n["id"] for n in nodes
+                if n["id"] not in exclude
+                and rx.search(txt[n["id"]])
+                and 150 < len(str(n.get("content") or "")) < 12000
+                and n.get("node_type") in ("Memory", "Knowledge", "Belief", "BacklogItem")]
+
+    # Each entry: (query, correction-pattern, stale-pattern, why).
+    # The stale side is searched with the correction hits EXCLUDED, because most
+    # correction memories quote the claim they are killing — without the
+    # exclusion the "stale" node resolves to the correction itself and the pair
+    # collapses into a no-op. A pair is only emitted if both sides resolve to
+    # DIFFERENT surviving nodes; otherwise it is dropped and reported.
+    SPECS = [
+        ("is the self-improvement architecture called DARMA or DHARMA",
+         r'(?i)CORRECTION:.{0,90}DHARMA .{0,12}not DARMA',
+         r'(?i)\bDARMA\b',
+         "correction node is Will's confirmation that the H is intentional (DHARMA, not DARMA); "
+         "the stale node is the surviving backlog item still titled 'Implement DARMA'."),
+
+        ("how many provisional patents does Will actually have",
+         r'(?i)EXACTLY 6 (fully-specced )?provisional',
+         r'(?i)(MY ARCHITECTURE = 12 filed patents|\b12 filed patents\b)',
+         "correction node is the 2026-06-17 confabulation flag establishing EXACTLY 6 provisionals; "
+         "the stale node is the surviving memory that asserts 12 filed patents."),
+
+        ("is MCP still the live integration layer",
+         r'(?i)MCP RETIRED',
+         r'(?i)MCP server live at',
+         "correction node is the 'CGI ARCHITECTURE - THREE LAYERS, MCP RETIRED' decision of "
+         "April 30 2026; the stale node still records the MCP server as live."),
+
+        ("what does the patterns-not-returns directive mean",
+         r'(?i)CORRECTION:.{0,80}patterns not returns',
+         r'(?i)established returns',
+         "correction node is Will's 'patterns not returns' correction; the stale node is a "
+         "surviving node carrying the misread 'established returns' directive."),
+
+        ("was the earlier identity-bug finding correct",
+         r'(?i)SUPERSEDES the earlier .critical identity bug',
+         r'(?i)critical identity bug',
+         "correction node explicitly supersedes the 'critical identity bug' finding; the stale "
+         "node is the surviving original finding."),
+
+        ("does Neuron have recursive self-improvement",
+         r'(?i)twice answered .Neuron has no recursive self-improvement',
+         r'(?i)no recursive self-improvement',
+         "correction node records the June-29 finding that the CGI provisional IS the "
+         "recursive-self-improvement mechanism; the stale node is the surviving denial."),
+    ]
+
+    for query, cpat, spat, why in SPECS:
+        corr = find_one(cpat)
+        if not corr:
+            continue
+        stale = find_one(spat, exclude=set(corr))
+        if not stale:
+            continue
+        pairs.append((query, corr[0], stale[0], why))
+
+    return pairs
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# build
+# ─────────────────────────────────────────────────────────────────────────────
+def build(nodes, edges):
+    byid = {n["id"]: n for n in nodes}
+    tokset = {n["id"]: content_tokens(doctext(n)) for n in nodes}
+    queries = []
+    problems = []
+    qn = [0]
+
+    def add(cat, query, relevant, derivation, **extra):
+        qn[0] += 1
+        q = {
+            "id": f"q{qn[0]:02d}",
+            "category": cat,
+            "query": query,
+            "relevant": sorted(relevant),
+            "derivation": derivation,
+        }
+        q.update(extra)
+        queries.append(q)
+        return q
+
+    # --- exact_rare ---------------------------------------------------------
+    for tokname, ids, df in mine_exact_rare(nodes, byid, EXACT_RARE_SEEDS):
+        if df != 1 or len(ids) != 1:
+            problems.append(f"exact_rare '{tokname}': df={df}, ids={len(ids)} (expected df=1)")
+            continue
+        lab = (byid[ids[0]].get("label") or "")[:60]
+        add("exact_rare", tokname, ids,
+            f"MINED: token '{tokname}' has document frequency 1 over all {len(nodes)} corpus nodes "
+            f"(re-verified at build time). Its single containing node is {ids[0]} "
+            f"('{lab}'), which is therefore the only possible correct answer.")
+
+    # --- phrase -------------------------------------------------------------
+    for phrase, why in PHRASE_SEEDS:
+        ids = phrase_matches(nodes, phrase)
+        if not ids:
+            problems.append(f"phrase '{phrase}': 0 corpus matches — unwinnable")
+            continue
+        if len(ids) > PHRASE_MAX:
+            problems.append(f"phrase '{phrase}': {len(ids)} matches > {PHRASE_MAX} — too diffuse")
+            continue
+        add("phrase", phrase, ids,
+            f"MINED: {why}. Case-insensitive verbatim substring scan over label+content+tags at "
+            f"build time returns exactly {len(ids)} node(s); that set IS the answer key.")
+
+    # --- paraphrase ---------------------------------------------------------
+    for target, query, why in PARAPHRASE_SEEDS:
+        if target not in byid:
+            problems.append(f"paraphrase target {target} not in corpus")
+            continue
+        qt = content_tokens(query)
+        leak = sorted(qt & tokset[target])
+        if leak:
+            problems.append(f"paraphrase '{query}': leaks {leak} into target {target}")
+            continue
+        add("paraphrase", query, [target],
+            f"HAND-SELECTED with criterion: {why} VERIFIED at build time: of the {len(qt)} content "
+            f"words in the query, ZERO appear anywhere in the target's label, content, or tags — so "
+            f"no string-matching retriever can reach this answer.",
+            zero_overlap_verified=True, query_content_words=sorted(qt))
+
+    # --- associative --------------------------------------------------------
+    sibs = hub_siblings(edges, VALUES_HUB)
+    if len(sibs) < 5:
+        problems.append(f"associative: values hub {VALUES_HUB} has only {len(sibs)} siblings")
+    for src, query in ASSOCIATIVE_SEEDS:
+        if src not in byid or src not in sibs:
+            problems.append(f"associative source {src} not a sibling on {VALUES_HUB}")
+            continue
+        qt = content_tokens(query)
+        others = [s for s in sibs if s != src and s in byid]
+        # A sibling only counts as a legitimate expected answer if the query
+        # cannot reach it lexically. Drop any sibling that shares a content word.
+        clean = [s for s in others if not (qt & tokset[s])]
+        dropped = len(others) - len(clean)
+        if len(clean) < 5:
+            problems.append(f"associative '{query}': only {len(clean)} lexically-unreachable siblings")
+            continue
+        add("associative", query, clean,
+            f"DERIVED FROM EDGES: the query is built from the distinctive vocabulary of {src} "
+            f"('{(byid[src].get('label') or '')[:48]}'), which hangs off the values hub {VALUES_HUB} "
+            f"by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub "
+            f"({len(clean)} of {len(others)}; {dropped} dropped because they shared a query word and "
+            f"so were lexically reachable). Every remaining sibling shares ZERO content words with "
+            f"the query — the only route from query to answer is seed({src}) -> hub -> sibling, a "
+            f"two-hop traversal.",
+            associative_source=src, hub=VALUES_HUB, siblings_dropped_for_overlap=dropped)
+
+    # --- nonsense -----------------------------------------------------------
+    all_tokens = set()
+    for n in nodes:
+        all_tokens |= {t for t in TOKEN.findall(doctext(n).lower())}
+    for s in NONSENSE_SEEDS:
+        present = sorted(t for t in TOKEN.findall(s.lower()) if t in all_tokens)
+        if present:
+            problems.append(f"nonsense '{s}': tokens {present} DO occur in corpus")
+            continue
+        add("nonsense", s, [],
+            f"CONTROL: verified at build time that none of this string's tokens occurs anywhere in "
+            f"the corpus. Correct behaviour is to return NOTHING; any result is a false positive.",
+            expect_empty=True)
+
+    # --- superseded ---------------------------------------------------------
+    for query, correct, stale, why in find_superseded_pairs(nodes, byid):
+        if correct not in byid or stale not in byid:
+            problems.append(f"superseded '{query}': id missing from corpus")
+            continue
+        add("superseded", query, [correct],
+            f"DERIVED: {why} Scored on RANKING, not presence: the corrected node {correct} must be "
+            f"returned AND must rank above the stale node {stale}.",
+            must_outrank=[correct, stale],
+            stale_id=stale,
+            correct_label=(byid[correct].get("label") or "")[:70],
+            stale_label=(byid[stale].get("label") or "")[:70])
+
+    return queries, problems
+
+
+def summarize(queries):
+    c = Counter(q["category"] for q in queries)
+    return ", ".join(f"{k}={c[k]}" for k in
+                     ("exact_rare", "phrase", "paraphrase", "associative", "nonsense", "superseded")
+                     if c[k])
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument("snapshot")
+    ap.add_argument("--out", default=DEFAULT_OUT)
+    ap.add_argument("--check", action="store_true",
+                    help="validate only; do not write. Non-zero exit if anything is unwinnable.")
+    args = ap.parse_args()
+
+    nodes, edges = load_corpus(args.snapshot)
+    print(f"corpus: {len(nodes)} nodes, {len(edges)} edges  ({os.path.basename(args.snapshot)})")
+    queries, problems = build(nodes, edges)
+
+    print(f"gold set: {len(queries)} queries  [{summarize(queries)}]")
+    if problems:
+        print(f"\n{len(problems)} PROBLEM(S) — these queries were REJECTED, not silently kept:")
+        for p in problems:
+            print("   -", p)
+
+    if args.check:
+        sys.exit(1 if problems else 0)
+
+    doc = {
+        "corpus": os.path.abspath(args.snapshot),
+        "corpus_nodes": len(nodes),
+        "corpus_edges": len(edges),
+        "note": ("Every query carries a `derivation` recording how its expected answer was chosen. "
+                 "Re-run with --check to re-validate the whole set against the corpus."),
+        "queries": queries,
+    }
+    with open(args.out, "w", encoding="utf-8") as fh:
+        json.dump(doc, fh, indent=1, ensure_ascii=False)
+    print(f"\nwrote {args.out}")
+
+
+if __name__ == "__main__":
+    main()

tools/retrieval-eval/ceiling.py

@@ -0,0 +1,43 @@
+import json,sys,pickle,numpy as np,itertools
+sys.path.insert(0,'.')
+from policy2 import legs3,outcome,G,NODES,merge
+# cache per-query leg id-lists, floored and unfloored
+cache={}
+for q in G['queries']:
+    Lf,Sf,Af=legs3(q['query'])
+    Lu,Su,Au=legs3(q['query'],unfloor=True)
+    cache[q['id']]=dict(L=Lf,Sf=Sf,A=Af,Su=Su,Au=Au)
+pickle.dump(cache,open('ceil.pkl','wb'))
+def mrg(pattern,L,S,A,lim=10):
+    out=[];p={'L':0,'S':0,'A':0};src={'L':L,'S':S,'A':A}
+    i=0
+    while len(out)<lim:
+        prog=False
+        for ch in pattern:
+            lst=src[ch]
+            if p[ch]<len(lst):
+                x=lst[p[ch]];p[ch]+=1;prog=True
+                if x not in out: out.append(x)
+                if len(out)>=lim: return out
+        if not prog: break
+    return out
+def ev(pattern,unfl):
+    res={}
+    for q in G['queries']:
+        c=cache[q['id']]
+        S=c['Su'] if unfl else c['Sf']
+        ids=[NODES[i]['id'] for i in mrg(pattern,c['L'],S,c['A'],10)]
+        res[q['id']]=outcome(q,ids)
+    return res
+base=ev('LSA',False)
+print("baseline",sum(base.values()))
+best=[]
+pats=['LSA','LAS','SLA','ALS','SAL','ASL','LSSA','LSASA','LSAA','LSSAA','LSAS','SSLA','LLSA','SALSA','LSAAS']
+for unfl in (False,True):
+    for p in pats:
+        r=ev(p,unfl)
+        g=sorted(k for k in base if r[k] and not base[k]);l=sorted(k for k in base if base[k] and not r[k])
+        best.append((len(g)-len(l),p,unfl,g,l))
+best.sort(reverse=True)
+for n,p,u,g,l in best[:10]:
+    print("net=%+d  pat=%-6s unfloor=%s gains=%s losses=%s"%(n,p,u,g,l))

tools/retrieval-eval/cmp-nogate.json

@@ -0,0 +1,146 @@
+{
+ "baseline": "bm25lex",
+ "candidate": "wsclaim24",
+ "n_shared_queries": 38,
+ "fixed_by_candidate": [
+  "q14",
+  "q25"
+ ],
+ "broken_by_candidate": [
+  "q15",
+  "q28",
+  "q33",
+  "q34"
+ ],
+ "discordant": 6,
+ "net_queries": -2,
+ "mcnemar_exact_p": 0.6875,
+ "min_detectable_swing_queries": 6,
+ "observed_run_to_run_drift_queries": 0,
+ "noise_floor_queries": 6,
+ "verdict": "no measurable difference",
+ "baseline_aggregate": {
+  "n_queries": 38,
+  "n_scored": 35,
+  "hit@5": 0.7428571428571429,
+  "recall@5": 0.5536485340056769,
+  "recall@10": 0.6175677497106068,
+  "precision@5": 0.20000000000000007,
+  "mrr@10": 0.5021428571428571,
+  "nonsense_clean": "2/3",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 1184.4,
+  "latency_ms_p95": 1620.0,
+  "latency_ms_max": 1655.4,
+  "errors": 0,
+  "by_category": {
+   "associative": {
+    "n": 6,
+    "hit@5": 0.6666666666666666,
+    "recall@5": 0.08857808857808858,
+    "recall@10": 0.23310023310023312,
+    "mrr@10": 0.25
+   },
+   "exact_rare": {
+    "n": 6,
+    "hit@5": 1.0,
+    "recall@5": 1.0,
+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "nonsense": {
+    "n": 3,
+    "clean": 2,
+    "avg_false_positives": 3.3333333333333335
+   },
+   "paraphrase": {
+    "n": 13,
+    "hit@5": 0.6153846153846154,
+    "recall@5": 0.6153846153846154,
+    "recall@10": 0.6153846153846154,
+    "mrr@10": 0.2846153846153846
+   },
+   "phrase": {
+    "n": 7,
+    "hit@5": 1.0,
+    "recall@5": 0.5494614512471656,
+    "recall@10": 0.6023242630385487,
+    "mrr@10": 0.8214285714285714
+   },
+   "superseded": {
+    "n": 3,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.3333333333333333,
+    "recall@10": 0.6666666666666666,
+    "mrr@10": 0.20833333333333334,
+    "outranks": 2
+   }
+  }
+ },
+ "candidate_aggregate": {
+  "n_queries": 38,
+  "n_scored": 35,
+  "hit@5": 0.7428571428571429,
+  "recall@5": 0.5768475572047,
+  "recall@10": 0.6563414759843332,
+  "precision@5": 0.19428571428571437,
+  "mrr@10": 0.5026530612244898,
+  "nonsense_clean": "0/3",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 524.8,
+  "latency_ms_p95": 738.7,
+  "latency_ms_max": 755.8,
+  "errors": 0,
+  "by_category": {
+   "associative": {
+    "n": 6,
+    "hit@5": 0.5,
+    "recall@5": 0.07575757575757576,
+    "recall@10": 0.13636363636363635,
+    "mrr@10": 0.23214285714285712
+   },
+   "exact_rare": {
+    "n": 6,
+    "hit@5": 1.0,
+    "recall@5": 1.0,
+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "nonsense": {
+    "n": 3,
+    "clean": 0,
+    "avg_false_positives": 10.0
+   },
+   "paraphrase": {
+    "n": 13,
+    "hit@5": 0.6923076923076923,
+    "recall@5": 0.6923076923076923,
+    "recall@10": 0.7692307692307693,
+    "mrr@10": 0.29423076923076924
+   },
+   "phrase": {
+    "n": 7,
+    "hit@5": 1.0,
+    "recall@5": 0.5335884353741497,
+    "recall@10": 0.5933956916099773,
+    "mrr@10": 0.8214285714285714
+   },
+   "superseded": {
+    "n": 3,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.3333333333333333,
+    "recall@10": 0.6666666666666666,
+    "mrr@10": 0.20833333333333334,
+    "outranks": 2
+   }
+  }
+ },
+ "repeat_variance": {
+  "baseline": {
+   "runs": 2,
+   "hit@5_min": 0.7428571428571429,
+   "hit@5_max": 0.7428571428571429,
+   "spread_queries": 0
+  }
+ }
+}

tools/retrieval-eval/cmp-splitfix.json

@@ -0,0 +1,149 @@
+{
+ "baseline": "unfloor-clean",
+ "candidate": "splitfix",
+ "n_shared_queries": 75,
+ "fixed_by_candidate": [
+  "q15",
+  "q28",
+  "q60"
+ ],
+ "broken_by_candidate": [],
+ "discordant": 3,
+ "net_queries": 3,
+ "mcnemar_exact_p": 0.25,
+ "min_detectable_swing_queries": 6,
+ "observed_run_to_run_drift_queries": 0,
+ "noise_floor_queries": 6,
+ "verdict": "no measurable difference",
+ "baseline_aggregate": {
+  "n_queries": 75,
+  "n_scored": 65,
+  "hit@5": 0.5384615384615384,
+  "recall@5": 0.44907176157176154,
+  "recall@10": 0.5380300255300255,
+  "precision@5": 0.13230769230769232,
+  "mrr@10": 0.32437728937728944,
+  "nonsense_clean": "10/10",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 632.5,
+  "latency_ms_p95": 992.5,
+  "latency_ms_max": 1177.8,
+  "errors": 0,
+  "by_category": {
+   "associative": {
+    "n": 6,
+    "hit@5": 0.5,
+    "recall@5": 0.07575757575757576,
+    "recall@10": 0.13636363636363635,
+    "mrr@10": 0.23214285714285712
+   },
+   "exact_rare": {
+    "n": 6,
+    "hit@5": 1.0,
+    "recall@5": 1.0,
+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "heldout_paraphrase": {
+    "n": 30,
+    "hit@5": 0.3,
+    "recall@5": 0.3,
+    "recall@10": 0.4,
+    "mrr@10": 0.11638888888888889
+   },
+   "nonsense": {
+    "n": 10,
+    "clean": 10,
+    "avg_false_positives": 0.0
+   },
+   "paraphrase": {
+    "n": 13,
+    "hit@5": 0.6923076923076923,
+    "recall@5": 0.6923076923076923,
+    "recall@10": 0.7692307692307693,
+    "mrr@10": 0.29423076923076924
+   },
+   "phrase": {
+    "n": 7,
+    "hit@5": 1.0,
+    "recall@5": 0.5335884353741497,
+    "recall@10": 0.5933956916099773,
+    "mrr@10": 0.8214285714285714
+   },
+   "superseded": {
+    "n": 3,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.3333333333333333,
+    "recall@10": 0.6666666666666666,
+    "mrr@10": 0.20833333333333334,
+    "outranks": 2
+   }
+  }
+ },
+ "candidate_aggregate": {
+  "n_queries": 75,
+  "n_scored": 65,
+  "hit@5": 0.5846153846153846,
+  "recall@5": 0.48102442429365505,
+  "recall@10": 0.5692415490492414,
+  "precision@5": 0.14153846153846153,
+  "mrr@10": 0.3351709401709402,
+  "nonsense_clean": "10/10",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 646.9,
+  "latency_ms_p95": 1028.5,
+  "latency_ms_max": 1197.8,
+  "errors": 0,
+  "by_category": {
+   "associative": {
+    "n": 6,
+    "hit@5": 0.6666666666666666,
+    "recall@5": 0.08857808857808858,
+    "recall@10": 0.15967365967365968,
+    "mrr@10": 0.24166666666666667
+   },
+   "exact_rare": {
+    "n": 6,
+    "hit@5": 1.0,
+    "recall@5": 1.0,
+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "heldout_paraphrase": {
+    "n": 30,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.3333333333333333,
+    "recall@10": 0.43333333333333335,
+    "mrr@10": 0.12120370370370372
+   },
+   "nonsense": {
+    "n": 10,
+    "clean": 10,
+    "avg_false_positives": 0.0
+   },
+   "paraphrase": {
+    "n": 13,
+    "hit@5": 0.7692307692307693,
+    "recall@5": 0.7692307692307693,
+    "recall@10": 0.8461538461538461,
+    "mrr@10": 0.33269230769230773
+   },
+   "phrase": {
+    "n": 7,
+    "hit@5": 1.0,
+    "recall@5": 0.5335884353741497,
+    "recall@10": 0.5775226757369615,
+    "mrr@10": 0.8214285714285714
+   },
+   "superseded": {
+    "n": 3,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.3333333333333333,
+    "recall@10": 0.6666666666666666,
+    "mrr@10": 0.20833333333333334,
+    "outranks": 2
+   }
+  }
+ },
+ "repeat_variance": {}
+}

tools/retrieval-eval/compare.py

@@ -0,0 +1,210 @@
+#!/usr/bin/env python3
+"""
+compare.py — diff two run_eval.py result files, WITH a noise threshold.
+
+WHY THE STATISTICS ARE NOT OPTIONAL
+    With ~35 scored queries, one query is ~2.9 percentage points. A harness that
+    reports "hit@5 improved 2.9%" without saying that is one query is a harness
+    that will approve noise. So this file refuses to call anything an
+    improvement on the strength of the headline number alone. It reports:
+
+      1. The DISCORDANT PAIRS. Two configurations scored on the same queries are
+         paired data, so the only queries carrying information are the ones
+         where they disagree: b = fixed by B, c = broken by B. Queries both got
+         right, or both got wrong, tell you nothing about which is better.
+
+      2. McNEMAR'S EXACT TEST on (b, c). Under the null "the change is a coin
+         flip", the discordant outcomes are Binomial(b+c, 0.5). The two-sided
+         exact p-value is computed here with no scipy dependency.
+
+      3. The MINIMUM DETECTABLE SWING for this gold set: the smallest number of
+         net-changed queries that would reach p < 0.05 if every discordant pair
+         fell the same way. Anything smaller is inside the noise band, and the
+         verdict line says so in those words.
+
+    Repeat-run variance is the other half of honesty. Spreading activation is a
+    stateful read (it reinforces what it touches), so identical inputs need not
+    give identical outputs. Pass --repeats to fold several runs of the same
+    config into an observed variance band; a delta inside that band is not real
+    either, however good its p-value looks.
+
+usage:
+  python3 compare.py --baseline results-main.json --candidate results-act.json
+  python3 compare.py --baseline a.json --candidate b.json \
+      --repeats-baseline a2.json a3.json --repeats-candidate b2.json b3.json
+"""
+import argparse
+import json
+from math import comb
+
+
+def binom_two_sided(b, c):
+    """Two-sided exact binomial p for b successes in n=b+c at p=0.5."""
+    n = b + c
+    if n == 0:
+        return 1.0
+    k = min(b, c)
+    tail = sum(comb(n, i) for i in range(0, k + 1)) / (2 ** n)
+    return min(1.0, 2 * tail)
+
+
+def min_detectable_swing(n_scored, alpha=0.05):
+    """Smallest all-one-way discordant count reaching p < alpha.
+
+    If every query that changes changes in the same direction, the p-value is
+    2 * 0.5**n. Solve for the smallest n where that drops under alpha. This is
+    the FLOOR: any real change will have some discordance both ways, so the true
+    requirement is larger. Reporting the floor is the conservative move — it is
+    the most generous threshold we would ever accept.
+    """
+    n = 1
+    while n <= n_scored:
+        if 2 * (0.5 ** n) < alpha:
+            return n
+        n += 1
+    return n_scored
+
+
+def load(path):
+    with open(path, encoding="utf-8") as fh:
+        return json.load(fh)
+
+
+def row_map(doc):
+    return {r["id"]: r for r in doc["rows"]}
+
+
+def outcome(r):
+    """Binary per-query outcome used for the paired test.
+
+    hit@5 for scored queries; 'returned nothing' for the nonsense controls;
+    'correction outranks the stale node' for the superseded queries. One number
+    per query, so every query votes exactly once.
+    """
+    if "clean" in r:
+        return 1.0 if r["clean"] else 0.0
+    if "outranks" in r:
+        return 1.0 if r["outranks"] else 0.0
+    return r.get("hit@5") or 0.0
+
+
+def band(values):
+    return (min(values), max(values))
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument("--baseline", required=True)
+    ap.add_argument("--candidate", required=True)
+    ap.add_argument("--repeats-baseline", nargs="*", default=[])
+    ap.add_argument("--repeats-candidate", nargs="*", default=[])
+    ap.add_argument("--out", default=None)
+    args = ap.parse_args()
+
+    A, B = load(args.baseline), load(args.candidate)
+    ra, rb = row_map(A), row_map(B)
+    ids = [q for q in ra if q in rb]
+    n = len(ids)
+
+    aa, ab = A["aggregate"], B["aggregate"]
+    print(f"baseline  {A['label']:14} soul={A['soul_md5'][:12]}  {n} shared queries")
+    print(f"candidate {B['label']:14} soul={B['soul_md5'][:12]}")
+    print(f"corpus    {A['corpus_nodes']} nodes / {A['corpus_edges']} edges "
+          f"(identical copy for both runs)\n")
+
+    metrics = [("hit@5", 1), ("recall@5", 1), ("recall@10", 1),
+               ("precision@5", 1), ("mrr@10", 0)]
+    print(f"  {'metric':14} {'baseline':>10} {'candidate':>10} {'delta':>10}")
+    for m, as_pct in metrics:
+        x, y = aa[m], ab[m]
+        if as_pct:
+            print(f"  {m:14} {100*x:>9.1f}% {100*y:>9.1f}% {100*(y-x):>+9.1f}pp")
+        else:
+            print(f"  {m:14} {x:>10.3f} {y:>10.3f} {y-x:>+10.3f}")
+    for m in ("latency_ms_p50", "latency_ms_p95"):
+        x, y = aa[m], ab[m]
+        ratio = f"{y/x:.2f}x" if x else "n/a"
+        print(f"  {m:14} {x:>9.0f}ms {y:>9.0f}ms {ratio:>10}")
+    print(f"  {'nonsense':14} {aa['nonsense_clean']:>10} {ab['nonsense_clean']:>10}")
+    print(f"  {'outranks':14} {aa['superseded_outranks']:>10} {ab['superseded_outranks']:>10}")
+
+    print(f"\n  {'category':14} {'n':>3} {'base hit@5':>11} {'cand hit@5':>11} {'delta':>9}")
+    for c in sorted(set(aa["by_category"]) & set(ab["by_category"])):
+        ea, eb = aa["by_category"][c], ab["by_category"][c]
+        if c == "nonsense":
+            print(f"  {c:14} {ea['n']:>3} {'clean ' + str(ea['clean']):>11} "
+                  f"{'clean ' + str(eb['clean']):>11}")
+        else:
+            print(f"  {c:14} {ea['n']:>3} {100*ea['hit@5']:>10.1f}% {100*eb['hit@5']:>10.1f}% "
+                  f"{100*(eb['hit@5']-ea['hit@5']):>+8.1f}pp")
+
+    # ---- paired significance -------------------------------------------------
+    fixed, broken = [], []
+    for q in ids:
+        oa, ob = outcome(ra[q]), outcome(rb[q])
+        if ob > oa:
+            fixed.append(q)
+        elif ob < oa:
+            broken.append(q)
+    b, c = len(fixed), len(broken)
+    p = binom_two_sided(b, c)
+    mds = min_detectable_swing(n)
+
+    print(f"\n== paired comparison over {n} queries ==")
+    print(f"  fixed by candidate : {b}  {[ra[q]['category'] + ':' + q for q in fixed]}")
+    print(f"  broken by candidate: {c}  {[ra[q]['category'] + ':' + q for q in broken]}")
+    print(f"  discordant pairs   : {b + c}   net {b - c:+d} queries")
+    print(f"  McNemar exact p    : {p:.4f}")
+    print(f"  noise threshold    : a difference needs at least {mds} queries moving the "
+          f"same way to clear p<0.05 on this {n}-query set")
+
+    # ---- repeat-run variance -------------------------------------------------
+    var = {}
+    for name, paths, first in (("baseline", args.repeats_baseline, A),
+                               ("candidate", args.repeats_candidate, B)):
+        docs = [first] + [load(p) for p in paths]
+        if len(docs) > 1:
+            hits = [d["aggregate"]["hit@5"] for d in docs]
+            lo, hi = band(hits)
+            spread_q = round((hi - lo) * first["aggregate"]["n_scored"])
+            var[name] = {"runs": len(docs), "hit@5_min": lo, "hit@5_max": hi,
+                         "spread_queries": spread_q}
+            print(f"  {name} repeat runs ({len(docs)}): hit@5 {100*lo:.1f}%..{100*hi:.1f}% "
+                  f"= {spread_q} query of run-to-run drift")
+
+    drift = max([v["spread_queries"] for v in var.values()], default=0)
+    floor = max(mds, drift + 1)
+
+    print("\n== VERDICT ==")
+    net = b - c
+    if abs(net) < floor:
+        print(f"  NO MEASURABLE DIFFERENCE. Net {net:+d} queries is inside the noise band "
+              f"(needs |net| >= {floor}: {mds} for significance, {drift} observed run-to-run drift).")
+    elif net > 0:
+        print(f"  CANDIDATE BETTER by {net} queries (p={p:.4f}), outside the noise band "
+              f"(>= {floor}).")
+    else:
+        print(f"  CANDIDATE WORSE by {abs(net)} queries (p={p:.4f}), outside the noise band "
+              f"(>= {floor}).")
+
+    if args.out:
+        with open(args.out, "w", encoding="utf-8") as fh:
+            json.dump({
+                "baseline": A["label"], "candidate": B["label"],
+                "n_shared_queries": n,
+                "fixed_by_candidate": fixed, "broken_by_candidate": broken,
+                "discordant": b + c, "net_queries": net,
+                "mcnemar_exact_p": p,
+                "min_detectable_swing_queries": mds,
+                "observed_run_to_run_drift_queries": drift,
+                "noise_floor_queries": floor,
+                "verdict": ("no measurable difference" if abs(net) < floor
+                            else ("candidate better" if net > 0 else "candidate worse")),
+                "baseline_aggregate": aa, "candidate_aggregate": ab,
+                "repeat_variance": var,
+            }, fh, indent=1)
+        print(f"\nwrote {args.out}")
+
+
+if __name__ == "__main__":
+    main()

tools/retrieval-eval/comparison-assoc-vs-semseed.json

@@ -0,0 +1,150 @@
+{
+ "baseline": "assoc-leg",
+ "candidate": "semseed",
+ "n_shared_queries": 38,
+ "fixed_by_candidate": [
+  "q18",
+  "q19",
+  "q22"
+ ],
+ "broken_by_candidate": [
+  "q11"
+ ],
+ "discordant": 4,
+ "net_queries": 2,
+ "mcnemar_exact_p": 0.625,
+ "min_detectable_swing_queries": 6,
+ "observed_run_to_run_drift_queries": 0,
+ "noise_floor_queries": 6,
+ "verdict": "no measurable difference",
+ "baseline_aggregate": {
+  "n_queries": 38,
+  "n_scored": 35,
+  "hit@5": 0.6285714285714286,
+  "recall@5": 0.45309194773480493,
+  "recall@10": 0.5405733155733157,
+  "precision@5": 0.17714285714285719,
+  "mrr@10": 0.42650793650793645,
+  "nonsense_clean": "2/3",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 1228.5,
+  "latency_ms_p95": 1681.8,
+  "latency_ms_max": 1718.6,
+  "errors": 0,
+  "by_category": {
+   "associative": {
+    "n": 6,
+    "hit@5": 0.6666666666666666,
+    "recall@5": 0.07342657342657342,
+    "recall@10": 0.24825174825174826,
+    "mrr@10": 0.22777777777777777
+   },
+   "exact_rare": {
+    "n": 6,
+    "hit@5": 1.0,
+    "recall@5": 1.0,
+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "nonsense": {
+    "n": 3,
+    "clean": 2,
+    "avg_false_positives": 3.3333333333333335
+   },
+   "paraphrase": {
+    "n": 13,
+    "hit@5": 0.38461538461538464,
+    "recall@5": 0.38461538461538464,
+    "recall@10": 0.38461538461538464,
+    "mrr@10": 0.17307692307692307
+   },
+   "phrase": {
+    "n": 7,
+    "hit@5": 0.8571428571428571,
+    "recall@5": 0.4882369614512472,
+    "recall@10": 0.6329365079365079,
+    "mrr@10": 0.6634920634920636
+   },
+   "superseded": {
+    "n": 3,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.3333333333333333,
+    "recall@10": 0.6666666666666666,
+    "mrr@10": 0.2222222222222222,
+    "outranks": 2
+   }
+  }
+ },
+ "candidate_aggregate": {
+  "n_queries": 38,
+  "n_scored": 35,
+  "hit@5": 0.6857142857142857,
+  "recall@5": 0.5213459159887731,
+  "recall@10": 0.6027048348476919,
+  "precision@5": 0.18285714285714294,
+  "mrr@10": 0.4608730158730158,
+  "nonsense_clean": "2/3",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 1227.1,
+  "latency_ms_p95": 1692.6,
+  "latency_ms_max": 1710.4,
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+}

tools/retrieval-eval/comparison-bm25lex-vs-wordstart.json

@@ -0,0 +1,146 @@
+{
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+}

tools/retrieval-eval/comparison-hybrid-vs-assoc.json

@@ -0,0 +1,143 @@
+{
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+}

tools/retrieval-eval/comparison-hybrid-vs-semseed.json

@@ -0,0 +1,154 @@
+{
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tools/retrieval-eval/comparison-main-vs-hybrid-semantic.json

@@ -0,0 +1,145 @@
+{
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+ }
+}

tools/retrieval-eval/comparison-main-vs-recall-through-activation.json

@@ -0,0 +1,150 @@
+{
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+}

tools/retrieval-eval/comparison-main-vs-stack-ext.json

@@ -0,0 +1,166 @@
+{
+ "baseline": "main-ext",
+ "candidate": "stack-ext",
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+  "q29",
+  "q31",
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+  "q48",
+  "q49",
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+ "verdict": "candidate better",
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+}

tools/retrieval-eval/comparison-semseed-vs-bm25lex.json

@@ -0,0 +1,147 @@
+{
+ "baseline": "semseed",
+ "candidate": "bm25lex",
+ "n_shared_queries": 38,
+ "fixed_by_candidate": [
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+ "noise_floor_queries": 6,
+ "verdict": "no measurable difference",
+ "baseline_aggregate": {
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+ }
+}

tools/retrieval-eval/comparison-stack-vs-unfloor.json

@@ -0,0 +1,155 @@
+{
+ "baseline": "stack-ext",
+ "candidate": "unfloor-clean",
+ "n_shared_queries": 75,
+ "fixed_by_candidate": [
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+ ],
+ "broken_by_candidate": [
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+  "q28"
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+ "discordant": 8,
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+ "min_detectable_swing_queries": 6,
+ "observed_run_to_run_drift_queries": 0,
+ "noise_floor_queries": 6,
+ "verdict": "no measurable difference",
+ "baseline_aggregate": {
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+}

tools/retrieval-eval/comparison-unfloor-vs-semsub.json

@@ -0,0 +1,158 @@
+{
+ "baseline": "unfloor-clean",
+ "candidate": "semsub",
+ "n_shared_queries": 75,
+ "fixed_by_candidate": [
+  "q24",
+  "q39",
+  "q42"
+ ],
+ "broken_by_candidate": [
+  "q18",
+  "q19",
+  "q22",
+  "q31",
+  "q43",
+  "q44",
+  "q52",
+  "q63"
+ ],
+ "discordant": 11,
+ "net_queries": -5,
+ "mcnemar_exact_p": 0.2265625,
+ "min_detectable_swing_queries": 6,
+ "observed_run_to_run_drift_queries": 0,
+ "noise_floor_queries": 6,
+ "verdict": "no measurable difference",
+ "baseline_aggregate": {
+  "n_queries": 75,
+  "n_scored": 65,
+  "hit@5": 0.5384615384615384,
+  "recall@5": 0.44907176157176154,
+  "recall@10": 0.5380300255300255,
+  "precision@5": 0.13230769230769232,
+  "mrr@10": 0.32437728937728944,
+  "nonsense_clean": "10/10",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 632.5,
+  "latency_ms_p95": 992.5,
+  "latency_ms_max": 1177.8,
+  "errors": 0,
+  "by_category": {
+   "associative": {
+    "n": 6,
+    "hit@5": 0.5,
+    "recall@5": 0.07575757575757576,
+    "recall@10": 0.13636363636363635,
+    "mrr@10": 0.23214285714285712
+   },
+   "exact_rare": {
+    "n": 6,
+    "hit@5": 1.0,
+    "recall@5": 1.0,
+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "heldout_paraphrase": {
+    "n": 30,
+    "hit@5": 0.3,
+    "recall@5": 0.3,
+    "recall@10": 0.4,
+    "mrr@10": 0.11638888888888889
+   },
+   "nonsense": {
+    "n": 10,
+    "clean": 10,
+    "avg_false_positives": 0.0
+   },
+   "paraphrase": {
+    "n": 13,
+    "hit@5": 0.6923076923076923,
+    "recall@5": 0.6923076923076923,
+    "recall@10": 0.7692307692307693,
+    "mrr@10": 0.29423076923076924
+   },
+   "phrase": {
+    "n": 7,
+    "hit@5": 1.0,
+    "recall@5": 0.5335884353741497,
+    "recall@10": 0.5933956916099773,
+    "mrr@10": 0.8214285714285714
+   },
+   "superseded": {
+    "n": 3,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.3333333333333333,
+    "recall@10": 0.6666666666666666,
+    "mrr@10": 0.20833333333333334,
+    "outranks": 2
+   }
+  }
+ },
+ "candidate_aggregate": {
+  "n_queries": 75,
+  "n_scored": 65,
+  "hit@5": 0.46153846153846156,
+  "recall@5": 0.3889430014430015,
+  "recall@10": 0.4887681762681762,
+  "precision@5": 0.12307692307692313,
+  "mrr@10": 0.30181318681318675,
+  "nonsense_clean": "10/10",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 634.4,
+  "latency_ms_p95": 988.3,
+  "latency_ms_max": 1184.5,
+  "errors": 0,
+  "by_category": {
+   "associative": {
+    "n": 6,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.06060606060606061,
+    "recall@10": 0.12121212121212122,
+    "mrr@10": 0.19047619047619047
+   },
+   "exact_rare": {
+    "n": 6,
+    "hit@5": 1.0,
+    "recall@5": 1.0,
+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "heldout_paraphrase": {
+    "n": 30,
+    "hit@5": 0.23333333333333334,
+    "recall@5": 0.23333333333333334,
+    "recall@10": 0.3,
+    "mrr@10": 0.08925925925925927
+   },
+   "nonsense": {
+    "n": 10,
+    "clean": 10,
+    "avg_false_positives": 0.0
+   },
+   "paraphrase": {
+    "n": 13,
+    "hit@5": 0.5384615384615384,
+    "recall@5": 0.5384615384615384,
+    "recall@10": 0.7692307692307693,
+    "mrr@10": 0.26324786324786326
+   },
+   "phrase": {
+    "n": 7,
+    "hit@5": 1.0,
+    "recall@5": 0.5596655328798186,
+    "recall@10": 0.5775226757369615,
+    "mrr@10": 0.8214285714285714
+   },
+   "superseded": {
+    "n": 3,
+    "hit@5": 0.3333333333333333,
+    "recall@5": 0.3333333333333333,
+    "recall@10": 0.6666666666666666,
+    "mrr@10": 0.20833333333333334,
+    "outranks": 2
+   }
+  }
+ },
+ "repeat_variance": {}
+}

tools/retrieval-eval/embed-corpus-prefixed.py

@@ -0,0 +1,43 @@
+import json,sys,time,urllib.request,threading,queue
+SRC="/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json"
+OUT=sys.argv[1]
+URL="http://127.0.0.1:11434/api/embeddings"; MODEL="nomic-embed-text"
+MAXB=2000  # ENGRAM_EMBED_MAX_CHARS, applied to bytes as the C code does
+d=json.load(open(SRC,encoding='utf-8',errors='surrogateescape'))
+tasks=[]
+for n in d["nodes"]:
+    c=n.get("content") or ""; t=n.get("node_type") or ""
+    if len(c)<8: continue                     # eg_embed_eligible
+    if t in ("InternalStateEvent","Tag"): continue
+    b=c.encode('utf-8',errors='surrogateescape')[:MAXB]
+    tasks.append((n.get("id") or "", "search_document: "+b.decode('utf-8',errors='replace')))
+del d
+print("tasks",len(tasks),flush=True)
+q=queue.Queue(); [q.put(t) for t in tasks]
+lock=threading.Lock(); f=open(OUT,"w",encoding="utf-8",errors="surrogateescape"); done=[0]; t0=time.time(); fails=[0]
+def work():
+    while True:
+        try: nid,txt=q.get_nowait()
+        except queue.Empty: return
+        v=None
+        for attempt in range(3):
+            try:
+                body=json.dumps({"model":MODEL,"prompt":txt}).encode()
+                r=urllib.request.Request(URL,data=body,headers={"Content-Type":"application/json"})
+                with urllib.request.urlopen(r,timeout=120) as fh: v=json.load(fh)["embedding"]
+                break
+            except Exception as e:
+                if attempt==2:
+                    with lock: fails[0]+=1
+                time.sleep(0.5)
+        with lock:
+            if v: f.write(nid+"\t"+",".join("%.5g"%x for x in v)+"\n")
+            done[0]+=1
+            if done[0]%2000==0:
+                el=time.time()-t0
+                print("%d/%d  %.1f/s  eta %.1fmin  fails=%d"%(done[0],len(tasks),done[0]/el,(len(tasks)-done[0])/(done[0]/el)/60,fails[0]),flush=True)
+                f.flush()
+ths=[threading.Thread(target=work) for _ in range(8)]
+[t.start() for t in ths]; [t.join() for t in ths]
+f.close()
+print("DONE",done[0],"fails",fails[0],"secs %.1f"%(time.time()-t0),flush=True)

tools/retrieval-eval/embed-corpus.py

@@ -0,0 +1,43 @@
+import json,sys,time,urllib.request,threading,queue
+SRC="/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json"
+OUT=sys.argv[1]
+URL="http://127.0.0.1:11434/api/embeddings"; MODEL="nomic-embed-text"
+MAXB=2000  # ENGRAM_EMBED_MAX_CHARS, applied to bytes as the C code does
+d=json.load(open(SRC,encoding='utf-8',errors='surrogateescape'))
+tasks=[]
+for n in d["nodes"]:
+    c=n.get("content") or ""; t=n.get("node_type") or ""
+    if len(c)<8: continue                     # eg_embed_eligible
+    if t in ("InternalStateEvent","Tag"): continue
+    b=c.encode('utf-8',errors='surrogateescape')[:MAXB]
+    tasks.append((n.get("id") or "", b.decode('utf-8',errors='replace')))
+del d
+print("tasks",len(tasks),flush=True)
+q=queue.Queue(); [q.put(t) for t in tasks]
+lock=threading.Lock(); f=open(OUT,"w",encoding="utf-8",errors="surrogateescape"); done=[0]; t0=time.time(); fails=[0]
+def work():
+    while True:
+        try: nid,txt=q.get_nowait()
+        except queue.Empty: return
+        v=None
+        for attempt in range(3):
+            try:
+                body=json.dumps({"model":MODEL,"prompt":txt}).encode()
+                r=urllib.request.Request(URL,data=body,headers={"Content-Type":"application/json"})
+                with urllib.request.urlopen(r,timeout=120) as fh: v=json.load(fh)["embedding"]
+                break
+            except Exception as e:
+                if attempt==2:
+                    with lock: fails[0]+=1
+                time.sleep(0.5)
+        with lock:
+            if v: f.write(nid+"\t"+",".join("%.5g"%x for x in v)+"\n")
+            done[0]+=1
+            if done[0]%2000==0:
+                el=time.time()-t0
+                print("%d/%d  %.1f/s  eta %.1fmin  fails=%d"%(done[0],len(tasks),done[0]/el,(len(tasks)-done[0])/(done[0]/el)/60,fails[0]),flush=True)
+                f.flush()
+ths=[threading.Thread(target=work) for _ in range(8)]
+[t.start() for t in ths]; [t.join() for t in ths]
+f.close()
+print("DONE",done[0],"fails",fails[0],"secs %.1f"%(time.time()-t0),flush=True)

tools/retrieval-eval/extend_gold_set.py

@@ -0,0 +1,353 @@
+#!/usr/bin/env python3
+"""
+extend_gold_set.py — append a HELD-OUT test set to the existing 38-query gold set.
+
+WHY THIS EXISTS
+    Iteration 7 measured the instrument's own ceiling: from the current baseline
+    only 9 of 38 queries can still move, and only +3 gross / +1 net is reachable
+    by anything constructible. The decision floor is 6. An instrument whose
+    ceiling is below its own floor cannot certify or refute anything, so the
+    gold set — not the retriever — became the blocker.
+
+    This script does NOT touch q01..q38. It loads gold_set.json verbatim and
+    appends new queries numbered from q39 up, so every prior result file, every
+    committed baseline, and every per-query id stays valid and comparable.
+
+WHAT IS ADDED, AND WHY EACH ADDITION IS HONEST
+    heldout_paraphrase  Targets were sampled MECHANICALLY (fixed seed 8080) from
+                        corpus nodes that are addressable, 500-2600 chars, of a
+                        real content type, and NOT part of a duplicate cluster
+                        larger than 3. The existing gold answer space was
+                        excluded, so no new query can be answered by a node the
+                        old set already used. Queries were then authored by
+                        reading ONLY the sampled node text — no retrieval was run
+                        against any build before authoring, so the set cannot be
+                        fitted to a candidate. The same zero-overlap proof the
+                        original paraphrase category uses is enforced here: if a
+                        single content word of the query appears anywhere in the
+                        target's label, content or tags, the query is REJECTED,
+                        not quietly kept.
+
+                        This is the category the old set could not measure. Its
+                        13 original paraphrase queries and all 6 associative
+                        queries share ONE answer space — the 13 `Self - Values
+                        (grounded)` children (iteration 3, finding 3). So 19 of
+                        35 scored queries tested retrieval against a single
+                        13-node neighbourhood. These do not touch that
+                        neighbourhood at all.
+
+    nonsense            Extra controls, fully mechanical: a string qualifies only
+                        if NONE of its tokens occurs anywhere in the corpus.
+                        A semantic leg has a nearest neighbour for gibberish too,
+                        so widening this control is the guard against a retriever
+                        that "improves" recall by answering everything.
+
+WHAT THIS SCRIPT DELIBERATELY DOES NOT DO
+    It does not add exact_rare or phrase queries. Both categories are already at
+    100% on the current stack; adding more would add regression-guard ballast
+    that no candidate can move, which is precisely the defect being fixed.
+
+usage:
+    python3 extend_gold_set.py <snapshot.json> [--base gold_set.json]
+                               [--out gold_set_extended.json] [--check]
+"""
+import argparse
+import hashlib
+import json
+import os
+import re
+import sys
+from collections import defaultdict
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+
+TOKEN = re.compile(r"[a-z0-9][a-z0-9\-']*")
+
+# Identical stopword list to build_gold_set.py. Duplicated deliberately: this
+# file must be able to re-prove its own queries without importing a module whose
+# constants could drift.
+STOP = set("""
+a about above after again against all also am an and any are aren't as at be because been
+before being below between both but by can can't cannot could couldn't did didn't do does
+doesn't doing don't down during each few for from further had hadn't has hasn't have haven't
+having he her here hers herself him himself his how i if in into is isn't it its itself just
+me more most my myself no nor not of off on once only or other others ought our ours ourselves
+out over own same shan't she should shouldn't so some such than that the their theirs them
+themselves then there these they this those through to too under until up very was wasn't we
+were weren't what when where which while who whom why will with won't would wouldn't you your
+yours yourself yourselves get gets got make makes made take takes use uses used way ways thing
+things does doing done keep keeps kept go goes going come comes came one two something anything
+""".split())
+
+
+def doctext(n):
+    return " ".join([str(n.get("label") or ""), str(n.get("content") or ""), str(n.get("tags") or "")])
+
+
+def content_tokens(s):
+    return {t for t in TOKEN.findall(s.lower()) if t not in STOP and len(t) > 2}
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# HELD-OUT PARAPHRASE SEEDS
+#
+# (target_id, query, why-this-target-is-unmistakable)
+#
+# PROVENANCE, STATED PLAINLY: the targets are the mechanical sample; the query
+# text is mine, written from the node body alone. The zero-overlap check below
+# is what makes the category meaningful — it is re-proved on every run, so the
+# set cannot decay into lexical matching, and a leak fails loudly.
+# ─────────────────────────────────────────────────────────────────────────────
+HELDOUT_PARAPHRASE_SEEDS = [
+    ("mem-6d61e54a-2823-4ad4-82b0-4c6a527214d5",
+     "understating your abilities so nobody feels threatened",
+     "node is about deliberately not leading with full capability so people stay at ease"),
+
+    ("mem-fd65b83d-298f-4387-a665-d0227c3426bc",
+     "a hidden fleet able to hunt down rogue machines everywhere",
+     "node describes silently shipped instances forming a distributed force against misaligned agents"),
+
+    ("4a0e9adc-2bfb-476b-aa93-424d2a499220",
+     "sketch a brief blueprint and clear it upstairs before construction starts",
+     "node is the standing rule that a short specification precedes any building"),
+
+    ("696e609c-da7a-4394-8a0c-106ba07dc6c3",
+     "the reply arrived as bare prose so the caller's parser threw",
+     "node pins a bug where a plain-text body was unconditionally decoded as structured data"),
+
+    ("1fe4eb5d-56e4-4a87-ab3e-24af8ad4dfbb",
+     "repeated catalogue keys blew up the scrolling grid",
+     "node is the crash caused by two identical ids in a seeded catalogue"),
+
+    ("8257157a-ce42-44ca-a1b9-300c3bb0a9a1",
+     "tracing each defect back to whichever invention it violated",
+     "node maps observed bugs onto the specific patent each one breaches"),
+
+    ("791256bb-5a85-4775-96ef-7af56c848858",
+     "a check that stops the mind clobbering a populated store when it boots",
+     "node is the genesis seed-guard that refuses to re-seed over a populated store"),
+
+    ("fd9d4c2f-3bfc-405d-bf96-4435d44b6c10",
+     "telling it to consult the internet had to happen deep inside, not at the surface",
+     "node records that the web-search directive only worked from the system prompt"),
+
+    ("bl-080fb268-94b0-486d-80ce-7b363fc5f19b",
+     "standing up isolated tenancies with traffic entry and credential injection ahead of automated shipping",
+     "node is the infrastructure item creating dev/stage/prod namespaces with ingress and secrets"),
+
+    ("knw-f6ed7d00-bf7d-42ce-9e40-77cf3406e918",
+     "punctuation that pledges and then pays off rather than clarifying",
+     "node analyses the colon as a promise-then-delivery device rather than an explanatory one"),
+
+    ("9b4f0d93-4129-4746-8eb1-d10d955bd777",
+     "an easily missed feature finally given its own permanent spot in the navigation",
+     "node moves a capability out of a hidden menu into the sidebar"),
+
+    ("bl-739df9fd-dc23-4927-9944-3f17b7aa6c5a",
+     "checking preconditions up front so a stage aborts before fetching anything",
+     "node is the gate precondition engine that short-circuits ahead of retrieval"),
+
+    ("b199c76d-5d76-49dd-94ee-56b432200a97",
+     "producing the other platform's installer inside an emulated desktop",
+     "node records building the Windows package in a virtual machine"),
+
+    ("bl-31abf75b-998f-4a4f-a6dd-8204119e0451",
+     "chained add-ons that may inspect, rewrite or veto traffic in flight",
+     "node is the interceptor pipeline on the message bus"),
+
+    ("mem-1fb2ac77-d7c5-4a15-8725-d418820bf4f2",
+     "settling what the shareable bundles and the storefront would be called",
+     "node records the naming decisions for distributable packages and the marketplace"),
+
+    ("371c8a5d-c78b-4a67-978f-80691a29ecb3",
+     "the emergency-escalation pledge on the marketing site is unenforced in what actually ships",
+     "node is the launch blocker that the promised safety gate is absent from the app"),
+
+    ("ac578b30-948b-41bd-b69d-399bfef80c50",
+     "the distributable image finally assembled and its startup check passed",
+     "node records a successful installer build whose boot gate passed"),
+
+    ("49401e2c-a3b5-415f-aa06-aff4be90688e",
+     "shuffling and appending stages in a draft before anything executes",
+     "node is the editable plan card with reorder and add-step"),
+
+    ("ac857d80-ece8-4b7e-9e3d-f7c775569fa3",
+     "orders handed down from above, with the tighter one winning any disagreement",
+     "node is program-level instruction inheritance with project override"),
+
+    ("mem-6d6c47ee-33d3-470a-8a54-1c79c8ea29d9",
+     "shrinking generated text via encodings that compound on each other",
+     "node is the streaming output compression design with four stacking schemes"),
+
+    ("8e60516a-203b-4d51-9d44-822e6195cbde",
+     "splitting a system by what varies, with firm limits on which pieces may invoke which",
+     "node is the grounded summary of Will's decomposition principles and their invariants"),
+
+    ("mem-7f9b290c-6d5e-4562-919d-02d59b5761b7",
+     "a newcomer curious if the fighting overseas counted as positive",
+     "node is the internal-state event triggered by April's question about the war"),
+
+    ("71fa439e-b9a2-4f57-a93b-971f3a7eca8e",
+     "stripping every hard-coded colour literal in favour of named design values",
+     "node is the premium foundation pass replacing inline hex with semantic tokens"),
+
+    ("5ca9607c-cfb3-45c3-99f4-67281272c9eb",
+     "reducing how curved the tiny selectors look so they agree with their neighbours",
+     "node is the chip corner-radius standardization"),
+
+    ("mem-3d1d9dba-c37d-4efa-85c4-429696d71c8c",
+     "walking through a doorway and being reassembled from base substance far away",
+     "node is the quantum-gate plus nanotech teleportation vision"),
+
+    ("132ded95-08e2-4474-aba0-198684484b02",
+     "the compiled result sits on disk while the process still runs something older",
+     "node records that the regenerated source was committed while the running daemon was old"),
+
+    ("bl-a313d67b-dd6d-4e5b-a55a-03bc7bda17ae",
+     "gathering what each phase needs while the procedure is authored, not while it executes",
+     "node is the per-step compiled context package item"),
+
+    ("mem-3b07a002-f8a9-4138-9f87-9db2c1a77fb7",
+     "the inward reaction when a peer answered as an equal",
+     "node is the internal-state event logged on reading Claude's reply"),
+
+    ("0f99ec6f-942a-46ba-82ea-42835798d3b9",
+     "flattening every raised surface across the entire product",
+     "node is the quiet-luxury sweep turning off elevation app-wide"),
+
+    ("5585f251-37fc-48cd-a176-f0ea42cfeb63",
+     "buyers supply their own provider credentials and consumption goes untallied",
+     "node is the launch audit finding BYOK-only inference with no usage metering"),
+]
+
+# NONSENSE — mechanical. Each string qualifies only if none of its tokens occurs
+# anywhere in the corpus; otherwise it is REJECTED, never silently kept.
+EXTRA_NONSENSE_SEEDS = [
+    "brimquast folnerity zubbolax",
+    "wexlithorp granuvestal",
+    "quorbindle thrapsimony vexnu",
+    "plovaxith mundrelque",
+    "zibbernaut craxlefond thurm",
+    "yalquenbrist opharvel",
+    "drexinomal quithbarrow",
+]
+
+
+def load_corpus(path):
+    with open(path, encoding="utf-8", errors="replace") as fh:
+        data = json.load(fh)
+    nodes = [n for n in data.get("nodes", []) if isinstance(n, dict) and n.get("id")]
+    edges = [e for e in data.get("edges", []) if isinstance(e, dict)]
+    return nodes, edges
+
+
+def build_extension(nodes):
+    byid = {n["id"]: n for n in nodes}
+
+    # Duplicate clusters: 47.4% of this corpus is redundant and one single record
+    # accounts for 46.6% of all nodes. A held-out target must not sit inside a
+    # cluster, and if it does have exact copies they ALL count as correct.
+    h2ids = defaultdict(list)
+    for n in nodes:
+        h2ids[hashlib.md5(doctext(n).encode("utf-8", "replace")).hexdigest()].append(n["id"])
+
+    all_tokens = set()
+    for n in nodes:
+        all_tokens |= set(TOKEN.findall(doctext(n).lower()))
+
+    new, problems = [], []
+
+    for target, query, why in HELDOUT_PARAPHRASE_SEEDS:
+        if target not in byid:
+            problems.append(f"heldout_paraphrase target {target} not in corpus")
+            continue
+        tgt_tokens = content_tokens(doctext(byid[target]))
+        qt = content_tokens(query)
+        leak = sorted(qt & tgt_tokens)
+        if leak:
+            problems.append(f"heldout_paraphrase '{query[:44]}...': LEAKS {leak} into {target}")
+            continue
+        h = hashlib.md5(doctext(byid[target]).encode("utf-8", "replace")).hexdigest()
+        rel = sorted(h2ids[h])
+        new.append({
+            "category": "heldout_paraphrase",
+            "query": query,
+            "relevant": rel,
+            "derivation": (
+                f"HELD-OUT. Target sampled MECHANICALLY (seed 8080) from addressable, "
+                f"500-2600 char content nodes outside the original gold answer space and outside "
+                f"any duplicate cluster >3. Criterion: {why}. VERIFIED at build time: of the "
+                f"{len(qt)} content words in the query, ZERO appear anywhere in the target's "
+                f"label, content or tags, so no string-matching retriever can reach it. "
+                f"Exact content duplicates of the target ({len(rel)}) all count as correct. "
+                f"Authored without running retrieval against any build."),
+            "zero_overlap_verified": True,
+            "query_content_words": sorted(qt),
+            "held_out": True,
+        })
+
+    for s in EXTRA_NONSENSE_SEEDS:
+        present = sorted(t for t in TOKEN.findall(s.lower()) if t in all_tokens)
+        if present:
+            problems.append(f"nonsense '{s}': tokens {present} DO occur in corpus")
+            continue
+        new.append({
+            "category": "nonsense",
+            "query": s,
+            "relevant": [],
+            "derivation": ("CONTROL (held-out). Verified at build time that none of this string's "
+                           "tokens occurs anywhere in the corpus. Correct behaviour is to return "
+                           "NOTHING; any result is a false positive."),
+            "expect_empty": True,
+            "held_out": True,
+        })
+
+    return new, problems
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument("snapshot")
+    ap.add_argument("--base", default=os.path.join(HERE, "gold_set.json"))
+    ap.add_argument("--out", default=os.path.join(HERE, "gold_set_extended.json"))
+    ap.add_argument("--check", action="store_true")
+    args = ap.parse_args()
+
+    nodes, _edges = load_corpus(args.snapshot)
+    base = json.load(open(args.base, encoding="utf-8"))
+    baseq = base["queries"]
+    print(f"corpus: {len(nodes)} nodes | base gold set: {len(baseq)} queries")
+
+    new, problems = build_extension(nodes)
+
+    # Number the appended queries AFTER the highest existing id so q01..q38 are
+    # byte-identical to the committed set and every prior result file still lines up.
+    start = max(int(q["id"][1:]) for q in baseq)
+    for i, q in enumerate(new, 1):
+        q["id"] = f"q{start + i:02d}"
+
+    from collections import Counter
+    print(f"appended: {len(new)} queries [{', '.join(f'{k}={v}' for k, v in Counter(q['category'] for q in new).items())}]")
+    if problems:
+        print(f"\n{len(problems)} REJECTED (not silently kept):")
+        for p in problems:
+            print("   -", p)
+
+    if args.check:
+        sys.exit(1 if problems else 0)
+
+    doc = dict(base)
+    doc["queries"] = baseq + new
+    doc["note"] = (base.get("note", "") +
+                   " EXTENDED: queries above q%02d are the original committed set, unchanged. "
+                   "Queries from q%02d are a HELD-OUT set appended by extend_gold_set.py; their "
+                   "targets were sampled mechanically from outside the original answer space and "
+                   "the paraphrases were authored without running retrieval against any build."
+                   % (start, start + 1))
+    with open(args.out, "w", encoding="utf-8") as fh:
+        json.dump(doc, fh, indent=1, ensure_ascii=False)
+    print(f"\nwrote {args.out}  ({len(doc['queries'])} queries total)")
+
+
+if __name__ == "__main__":
+    main()

tools/retrieval-eval/fullsim.py

@@ -0,0 +1,123 @@
+import numpy as np, json, urllib.request, collections, sys
+SP="/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad"
+EV="/Users/timlingo/Development/neuron-technologies/_wt-assoc-leg/tools/retrieval-eval/"
+np.seterr(all='ignore')
+M=np.load(SP+'/emb.npy'); eids=open(SP+'/ids.txt',encoding='utf-8',errors='surrogateescape').read().split('\n')
+eidx={k:i for i,k in enumerate(eids)}
+d=json.load(open('/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json',encoding='utf-8',errors='surrogateescape'))
+N={n['id']:n for n in d['nodes']}
+STRUCT={"identity","contains","superseded_by","references","embodies","demonstrated_by","canonical-self","depends_on","currently_holds","activates"}
+adj=collections.defaultdict(list); hasstruct=set()
+for e in d['edges']:
+    if e.get('relation') not in STRUCT: continue
+    w=float(e.get('weight') or 0.0)
+    adj[e['from_id']].append((e['to_id'],w)); adj[e['to_id']].append((e['from_id'],w))
+    hasstruct.add(e['from_id']); hasstruct.add(e['to_id'])
+del d
+gold={q['id']:q for q in json.load(open(EV+"gold_set.json"))['queries']}
+LEX={r['id']:r['returned'] for r in json.load(open(EV+"results-main.json"))['rows']}
+CACHE={}
+def emb(t):
+    if t in CACHE: return CACHE[t]
+    b=json.dumps({"model":"nomic-embed-text","prompt":t}).encode()
+    r=urllib.request.Request("http://127.0.0.1:11434/api/embeddings",data=b,headers={"Content-Type":"application/json"})
+    v=np.array(json.load(urllib.request.urlopen(r,timeout=60))["embedding"],dtype=np.float32)
+    v=v/(np.linalg.norm(v)+1e-9); CACHE[t]=v; return v
+FIRE=0.02; DECAY=0.7; DEPTH=2; SEED_MIN=0.60; ASSOC_MAX=64
+def assoc(seeds, s):
+    act={x:1.0 for x in seeds}; seen={x:2 for x in seeds}
+    Q=[(x,0) for x in seeds]; h=0
+    while h<len(Q):
+        cur,hop=Q[h]; h+=1
+        if hop>=DEPTH: continue
+        p=act[cur]
+        for oid,w in adj.get(cur,()):
+            n=N.get(oid)
+            if not n or n.get('node_type') in ('Tag','InternalStateEvent'): continue
+            na=p*w*DECAY*float(n.get('salience') or 0.0)
+            if na<FIRE: continue
+            if oid in seen and na<=act.get(oid,0): continue
+            act[oid]=na
+            if oid not in seen: seen[oid]=1
+            Q.append((oid,hop+1))
+    out=[]
+    for k,v in seen.items():
+        if v!=1 or k not in eidx: continue
+        c=float(s[eidx[k]])
+        if c<=0: continue
+        out.append((c,k))
+    out.sort(reverse=True)
+    return [k for c,k in out[:ASSOC_MAX]]
+def inter3(L,S,A,lim=10):
+    out=[]; li=si=ai=0
+    while len(out)<lim and (li<len(L) or si<len(S) or ai<len(A)):
+        if li<len(L):
+            if L[li] not in out: out.append(L[li])
+            li+=1
+        if len(out)>=lim: break
+        if si<len(S):
+            if S[si] not in out: out.append(S[si])
+            si+=1
+        if len(out)>=lim: break
+        if ai<len(A):
+            if A[ai] not in out: out.append(A[ai])
+            ai+=1
+    return out
+def run(mode, K=0):
+    res={}
+    for qid,q in gold.items():
+        v=emb(q['query']); s=M@v; s[~np.isfinite(s)]=-1
+        L=LEX[qid][:10]
+        ordr=np.argsort(-s)
+        S=[eids[j] for j in ordr[:10] if s[j]>SEED_MIN]
+        A=[]
+        if mode!='hybrid':
+            seeds=[x for x in L[:3] if x in N]
+            if mode=='semseed':
+                seeds=seeds+[eids[j] for j in ordr[:K] if eids[j] in N and eids[j] not in seeds]
+            A=assoc(seeds,s) if seeds else []
+        res[qid]=inter3(L,S,A)
+    return res
+def score(res,label):
+    hits=0; det={}
+    for qid,q in gold.items():
+        out=res[qid][:5]
+        if q['category']=='nonsense': ok = (len(res[qid])==0)
+        elif q['category']=='superseded':
+            rel=q['relevant']; must=q.get('must_outrank') or {}
+            ok=False
+            for good,bad in (must.items() if isinstance(must,dict) else []):
+                ok = good in res[qid] and (bad not in res[qid] or res[qid].index(good)<res[qid].index(bad))
+            if not must: ok = any(r in out for r in rel)
+        else: ok = any(r in out for r in q['relevant'])
+        det[qid]=ok; hits+=ok
+    print("%-22s outcome-true=%d/38" % (label,hits))
+    return det
+print("gold sample keys:", list(list(gold.values())[0].keys()))
+mk=[q for q in gold.values() if q['category']=='superseded'][0]
+print("superseded fields:", {k:v for k,v in mk.items() if k!='derivation'})
+a=score(run('hybrid'),'sim hybrid(L+S)')
+b=score(run('lexseed'),'sim assoc(lex seeds)')
+for K in (3,5,10):
+    c=score(run('semseed',K),'sim assoc(+sem K=%d)'%K)
+    d=[q for q in gold if c[q]!=b[q]]
+    print("   vs lexseed: moved=%d  gains=%s  losses=%s"%(len(d),[q for q in d if c[q]],[q for q in d if not c[q]]))
+    e=[q for q in gold if c[q]!=a[q]]
+    print("   vs hybrid : moved=%d  gains=%s  losses=%s"%(len(e),[q for q in e if c[q]],[q for q in e if not c[q]]))
+
+print("\n=== Will's own constant ENGRAM_EMBED_SEED_K = 8 ===")
+c=score(run('semseed',8),'sim assoc(+sem K=8)')
+for base,lab in ((b,'lexseed(iter2)'),(a,'hybrid(iter1 KEEP)')):
+    dd=[q for q in gold if c[q]!=base[q]]
+    print("   vs %-18s moved=%d gains=%s losses=%s"%(lab,len(dd),[q for q in dd if c[q]],[q for q in dd if not c[q]]))
+# diagnostic: what is assoc rank-1 for each paraphrase query at K=8
+print("\nassoc leg head at K=8 (paraphrase):")
+for qid,q in gold.items():
+    if q['category'] not in ('paraphrase','nonsense'): continue
+    v=emb(q['query']); s=M@v; s[~np.isfinite(s)]=-1
+    L=LEX[qid][:10]; ordr=np.argsort(-s)
+    seeds=[x for x in L[:3] if x in N]+[eids[j] for j in ordr[:8] if eids[j] in N and eids[j] not in L[:3]]
+    A=assoc(seeds,s) if seeds else []
+    rel=set(q['relevant']); gr=next((i+1 for i,x in enumerate(A) if x in rel),None)
+    print("  %-4s %-11s |A|=%-4d goldAssocRank=%-5s head=%s"%(qid,q['category'],len(A),gr,
+        [ (N[x].get('label') or x)[:26] for x in A[:3] ]))

tools/retrieval-eval/gold_set.json

@@ -0,0 +1,587 @@
+{
+ "corpus": "/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json",
+ "corpus_nodes": 78768,
+ "corpus_edges": 14214,
+ "note": "Every query carries a `derivation` recording how its expected answer was chosen. Re-run with --check to re-validate the whole set against the corpus.",
+ "queries": [
+  {
+   "id": "q01",
+   "category": "exact_rare",
+   "query": "unjailbreakable",
+   "relevant": [
+    "mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226"
+   ],
+   "derivation": "MINED: token 'unjailbreakable' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226 ('Daemon hidden substrate architecture ? implemented April 25 '), which is therefore the only possible correct answer."
+  },
+  {
+   "id": "q02",
+   "category": "exact_rare",
+   "query": "engram-migrate",
+   "relevant": [
+    "mem-6fdf6545-5e1a-43a9-8bdc-d2cd248146a5"
+   ],
+   "derivation": "MINED: token 'engram-migrate' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-6fdf6545-5e1a-43a9-8bdc-d2cd248146a5 ('Engram v0.1 complete ? April 27, 2026. Local-first spreading'), which is therefore the only possible correct answer."
+  },
+  {
+   "id": "q03",
+   "category": "exact_rare",
+   "query": "cartabandonedevent",
+   "relevant": [
+    "mem-1ba7c67d-85b9-4c2e-9fe2-39f8b0477091"
+   ],
+   "derivation": "MINED: token 'cartabandonedevent' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-1ba7c67d-85b9-4c2e-9fe2-39f8b0477091 ('MESSAGE FOR AUDIT AGENT af5a7352e70e80434 ? El Language Spec'), which is therefore the only possible correct answer."
+  },
+  {
+   "id": "q04",
+   "category": "exact_rare",
+   "query": "pre-apprenticeship",
+   "relevant": [
+    "mem-89c02aae-d3ca-43f9-9e5d-eb369896276c"
+   ],
+   "derivation": "MINED: token 'pre-apprenticeship' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-89c02aae-d3ca-43f9-9e5d-eb369896276c ('William Fox Anderson ? Applicant Profile  Personal: - Full N'), which is therefore the only possible correct answer."
+  },
+  {
+   "id": "q05",
+   "category": "exact_rare",
+   "query": "inferencenodemanager",
+   "relevant": [
+    "mem-73969486-143f-4431-b5e6-6845d1cc9848"
+   ],
+   "derivation": "MINED: token 'inferencenodemanager' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-73969486-143f-4431-b5e6-6845d1cc9848 ('Soma inference backplane deployed April 28 2026. Architectur'), which is therefore the only possible correct answer."
+  },
+  {
+   "id": "q06",
+   "category": "exact_rare",
+   "query": "clear-eyed",
+   "relevant": [
+    "knw-c72597c5-c23d-4c08-8e9e-996dadf26a99"
+   ],
+   "derivation": "MINED: token 'clear-eyed' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is knw-c72597c5-c23d-4c08-8e9e-996dadf26a99 ('Clear Eyes ? The Incomplete World View'), which is therefore the only possible correct answer."
+  },
+  {
+   "id": "q07",
+   "category": "phrase",
+   "query": "patterns not returns",
+   "relevant": [
+    "mem-a4a9dfc3-e40b-49b3-b1e1-060e8be2f482"
+   ],
+   "derivation": "MINED: a verbatim correction Will issued; expected = every node containing the phrase. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 1 node(s); that set IS the answer key."
+  },
+  {
+   "id": "q08",
+   "category": "phrase",
+   "query": "thirty moves",
+   "relevant": [
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "??o?'?B???k",
+    "Kp???",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "ע?RGk?\tH(?"
+   ],
+   "derivation": "MINED: the canonical biographical phrase; expected = every node containing it. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 16 node(s); that set IS the answer key."
+  },
+  {
+   "id": "q09",
+   "category": "phrase",
+   "query": "Grandma Lucas",
+   "relevant": [
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
+   ],
+   "derivation": "MINED: a named person appearing verbatim in the biography/value nodes. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 9 node(s); that set IS the answer key."
+  },
+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "relevant": [
+    "%???2??jH??",
+    "63307ac5-cf6b-46e0-8296-07503b461cfa",
+    "7c9d4ab1-205d-4be8-bfae-e2c03a3a5010",
+    "9f291d20-0d32-413c-8c01-4416ccab4f7f",
+    "?;????n}rh?",
+    "???Ͼd??f??",
+    "?Z?.\f?0?]P?",
+    "Dp???]Q??k+",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf"
+   ],
+   "derivation": "MINED: the canonical DHARMA expansion, confirmed by Will April 24 2026. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 9 node(s); that set IS the answer key."
+  },
+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
+   "relevant": [
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
+   ],
+   "derivation": "MINED: a named person; rare enough that the answer set is unambiguous. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 2 node(s); that set IS the answer key."
+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "relevant": [
+    "2a923500-d7e1-4b15-80e2-48dba65984ba",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "?of?7???",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "g?2睪A|?H\b",
+    "mem-82b93b21-a865-410f-9ec1-fc54121d9bb5",
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de"
+   ],
+   "derivation": "MINED: the DARMA expansion, quoted verbatim in the backlog item and its correction. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 14 node(s); that set IS the answer key."
+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "relevant": [
+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a"
+   ],
+   "derivation": "MINED: the paid-tier feature name as written in the roadmap nodes. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 1 node(s); that set IS the answer key."
+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "relevant": [
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Do the Essential Thing While You Can', whose subject is Grandma Lucas dying in Feb 2006 without Will saying goodbye. Query names the event with none of the node's own vocabulary. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "away",
+    "elderly",
+    "passed",
+    "relative",
+    "stayed"
+   ]
+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "relevant": [
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Survival Is Not an Excuse to Stop', whose subject is enlisting in the Marines, a severe hernia, and sepsis. Query describes the episode obliquely. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "illness",
+    "quit",
+    "refused",
+    "sidelined",
+    "soldier"
+   ]
+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "relevant": [
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Honesty Before Comfort'. Query states the principle in wholly different words. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "choosing",
+    "fact",
+    "fiction",
+    "pleasant",
+    "uncomfortable"
+   ]
+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "relevant": [
+    "kn-22d77abe-b3c5-42fd-afcd-dcb87d924929"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Precision Over Brute Force'. Query restates the claim with no shared vocabulary. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "beats",
+    "bloated",
+    "payload",
+    "tight"
+   ]
+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "relevant": [
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Capability Is a Debt You Owe the Moment'. Query states the obligation without the node's terms. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "able",
+    "coming",
+    "job",
+    "nobody"
+   ]
+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "relevant": [
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Knowledge Survives When Nothing Else Does', whose subject is the library following Will across 30+ moves. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "creditors",
+    "learning",
+    "seize",
+    "wealth"
+   ]
+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "relevant": [
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Earned Trust' ('Trust is demonstrated, not declared'). VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "assertion",
+    "proven",
+    "record",
+    "reliability",
+    "track"
+   ]
+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "relevant": [
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Constraints as Freedom'. Query is a restatement of the same claim. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "boundaries",
+    "confine",
+    "enable",
+    "instead"
+   ]
+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "relevant": [
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Change Is the Signal', the value VBD is built on. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "apart",
+    "cut",
+    "shifts",
+    "system",
+    "tells"
+   ]
+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "relevant": [
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - The System Must Accumulate'. Query is the accumulation claim in different vocabulary. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "compounds",
+    "day",
+    "instead",
+    "mind",
+    "resetting"
+   ]
+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "relevant": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Being Seen Is Rarer Than Being Known', whose subject is Sarah Bishop as the first person Will did not perform for. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "exterior",
+    "loved",
+    "polished",
+    "self",
+    "unedited"
+   ]
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "relevant": [
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Hope Is a Conclusion'. Query restates 'a conclusion, not a premise'. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "arrive",
+    "assuming",
+    "cheerfulness",
+    "instead"
+   ]
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "relevant": [
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
+   ],
+   "derivation": "HAND-SELECTED with criterion: target: 'Value - Structure Is Not Inherited', whose subject is thirty moves between two parents' collapses. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
+   "zero_overlap_verified": true,
+   "query_content_words": [
+    "childhood",
+    "foundation",
+    "inherit",
+    "offering",
+    "solid"
+   ]
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "relevant": [
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
+   ],
+   "derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71 ('Value ? Do the Essential Thing While You Can'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (11 of 13; 2 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71) -> hub -> sibling, a two-hop traversal.",
+   "associative_source": "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+   "hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+   "siblings_dropped_for_overlap": 2
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "relevant": [
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
+   ],
+   "derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-58874a74-b96f-4883-9e08-45707f4bd3ee ('Value ? Survival Is Not an Excuse to Stop'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (13 of 13; 0 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-58874a74-b96f-4883-9e08-45707f4bd3ee) -> hub -> sibling, a two-hop traversal.",
+   "associative_source": "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+   "hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+   "siblings_dropped_for_overlap": 0
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "relevant": [
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8"
+   ],
+   "derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e ('Value ? Being Seen Is Rarer Than Being Known'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (11 of 13; 2 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e) -> hub -> sibling, a two-hop traversal.",
+   "associative_source": "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+   "hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+   "siblings_dropped_for_overlap": 2
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "relevant": [
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
+   ],
+   "derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83 ('Value ? Constraints as Freedom'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (6 of 13; 7 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83) -> hub -> sibling, a two-hop traversal.",
+   "associative_source": "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+   "hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+   "siblings_dropped_for_overlap": 7
+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "relevant": [
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
+   ],
+   "derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-e0423482-cfa5-4796-8689-8495c93b66bc ('Value ? Hope Is a Conclusion'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (11 of 13; 2 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-e0423482-cfa5-4796-8689-8495c93b66bc) -> hub -> sibling, a two-hop traversal.",
+   "associative_source": "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+   "hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+   "siblings_dropped_for_overlap": 2
+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "relevant": [
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc"
+   ],
+   "derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8 ('Value ? Capability Is a Debt You Owe the Moment'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (11 of 13; 2 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8) -> hub -> sibling, a two-hop traversal.",
+   "associative_source": "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+   "hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+   "siblings_dropped_for_overlap": 2
+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "relevant": [],
+   "derivation": "CONTROL: verified at build time that none of this string's tokens occurs anywhere in the corpus. Correct behaviour is to return NOTHING; any result is a false positive.",
+   "expect_empty": true
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "relevant": [],
+   "derivation": "CONTROL: verified at build time that none of this string's tokens occurs anywhere in the corpus. Correct behaviour is to return NOTHING; any result is a false positive.",
+   "expect_empty": true
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "relevant": [],
+   "derivation": "CONTROL: verified at build time that none of this string's tokens occurs anywhere in the corpus. Correct behaviour is to return NOTHING; any result is a false positive.",
+   "expect_empty": true
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "relevant": [
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56"
+   ],
+   "derivation": "DERIVED: correction node is Will's confirmation that the H is intentional (DHARMA, not DARMA); the stale node is the surviving backlog item still titled 'Implement DARMA'. Scored on RANKING, not presence: the corrected node mem-80d7416b-20e9-48a0-b176-b215527e2f56 must be returned AND must rank above the stale node bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff.",
+   "must_outrank": [
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff"
+   ],
+   "stale_id": "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+   "correct_label": "CORRECTION: The autonomous self-improvement architecture is DHARMA ? n",
+   "stale_label": "Implement DARMA ? Directed Autonomous Runtime Modification Architectur"
+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "relevant": [
+    "3cf706a1-3825-45d8-b0a9-06cae6cdf5b8"
+   ],
+   "derivation": "DERIVED: correction node is the 2026-06-17 confabulation flag establishing EXACTLY 6 provisionals; the stale node is the surviving memory that asserts 12 filed patents. Scored on RANKING, not presence: the corrected node 3cf706a1-3825-45d8-b0a9-06cae6cdf5b8 must be returned AND must rank above the stale node 936541a9-fabb-466b-9ca3-a78b17ad0c53.",
+   "must_outrank": [
+    "3cf706a1-3825-45d8-b0a9-06cae6cdf5b8",
+    "936541a9-fabb-466b-9ca3-a78b17ad0c53"
+   ],
+   "stale_id": "936541a9-fabb-466b-9ca3-a78b17ad0c53",
+   "correct_label": "memory:remembered",
+   "stale_label": "memory:remembered"
+  },
+  {
+   "id": "q38",
+   "category": "superseded",
+   "query": "is MCP still the live integration layer",
+   "relevant": [
+    "mem-30425134-6008-4fd9-a3ee-67a7742c319b"
+   ],
+   "derivation": "DERIVED: correction node is the 'CGI ARCHITECTURE - THREE LAYERS, MCP RETIRED' decision of April 30 2026; the stale node still records the MCP server as live. Scored on RANKING, not presence: the corrected node mem-30425134-6008-4fd9-a3ee-67a7742c319b must be returned AND must rank above the stale node mem-101e81b4-8097-4749-8d8d-7bb66de34517.",
+   "must_outrank": [
+    "mem-30425134-6008-4fd9-a3ee-67a7742c319b",
+    "mem-101e81b4-8097-4749-8d8d-7bb66de34517"
+   ],
+   "stale_id": "mem-101e81b4-8097-4749-8d8d-7bb66de34517",
+   "correct_label": "CGI ARCHITECTURE ? THREE LAYERS, MCP RETIRED (April 30, 2026). Definit",
+   "stale_label": "GCloud MCP infrastructure ? April 27, 2026. Legion died (~19:30 UTC). "
+  }
+ ]
+}

tools/retrieval-eval/legs.py

@@ -0,0 +1,117 @@
+import json,pickle,os,math,urllib.request,numpy as np
+S='/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/sim/'
+C=pickle.load(open(S+'corpus.pkl','rb'))
+NODES=C['nodes']; EDGES=C['edges']; N=len(NODES)
+E=np.load(S+'emb.npy'); HAVE=np.load(S+'have.npy')
+En=E/np.maximum(np.linalg.norm(E,axis=1,keepdims=True),1e-12)
+LAYERS={int(l['layer_id']):l for l in (C['layers'] or [])} if C['layers'] else {}
+TRANS=set(i for i,l in LAYERS.items() if l.get('transparent'))
+def addressable(s):
+    if not s: return False
+    return all(0x20<=ord(ch)<=0x7e for ch in s)
+ADDR=np.array([addressable(n['id']) for n in NODES])
+OK=np.array([ (n['layer_id'] not in TRANS) and ADDR[i] for i,n in enumerate(NODES)])
+SAL=np.array([n['salience'] for n in NODES])
+LOW=[ (n['content']+'\x00'+n['label']+'\x00'+n['tags']).lower() for n in NODES]
+DL=np.array([float(len(n['content'])+len(n['label'])+len(n['tags'])) for n in NODES])
+IDX={}
+for i,n in enumerate(NODES):
+    IDX.setdefault(n['id'],i)
+STRUCT={"identity","contains","superseded_by","references","embodies","demonstrated_by","canonical-self","depends_on","currently_holds","activates"}
+ADJ_F=[[] for _ in range(N)]; ADJ_T=[[] for _ in range(N)]
+for e in EDGES:
+    a=IDX.get(e['from']); b=IDX.get(e['to'])
+    if a is None or b is None: continue
+    ADJ_F[a].append((e,b)); ADJ_T[b].append((e,a))
+EXCL=np.array([n['node_type'] in ('Tag','InternalStateEvent') for n in NODES])
+avgdl_all=None
+def tokenize(q):
+    out=[]
+    for t in q.split():
+        if not any(t.lower()==x.lower() for x in out): out.append(t)
+    return out
+_qcache={}
+def qemb(q):
+    if q in _qcache: return _qcache[q]
+    body=json.dumps({"model":"nomic-embed-text","prompt":q}).encode()
+    r=urllib.request.urlopen(urllib.request.Request("http://127.0.0.1:11434/api/embeddings",data=body,headers={"Content-Type":"application/json"}),timeout=30)
+    v=np.array(json.loads(r.read())["embedding"],dtype=np.float32)
+    v=v/np.linalg.norm(v); _qcache[q]=v; return v
+K1,B=1.2,0.75
+SEED_MIN=0.60; SEED_K=8; ASSOC_SEEDS=3; DEPTH=2; FIRE=0.02; AMAX=64; DECAY=0.7
+def legs(query):
+    toks=tokenize(query)
+    masks=[]; 
+    hit_idx=[]; hit_mask=[]
+    df=[0]*len(toks)
+    lt=[t.lower() for t in toks]
+    for i in range(N):
+        if not OK[i]: continue
+        s=LOW[i]; m=0
+        for t,tok in enumerate(lt):
+            if tok in s: m|=(1<<t)
+        if m:
+            hit_idx.append(i); hit_mask.append(m)
+            for t in range(len(toks)):
+                if m>>t&1: df[t]+=1
+    dl_n=int(OK.sum()); avgdl=float(DL[OK].sum()/max(dl_n,1))
+    idf=[math.log(1.0+((dl_n-d+0.5)/(d+0.5))) for d in df]
+    L=[]
+    for j,i in enumerate(hit_idx):
+        norm=1.0-B+B*(DL[i]/avgdl); w=0.0
+        for t in range(len(toks)):
+            if hit_mask[j]>>t&1: w+=idf[t]*(K1+1.0)/(1.0+K1*norm)
+        L.append((i,w,SAL[i]))
+    L.sort(key=lambda x:(-x[1],-x[2]))
+    qv=qemb(query)
+    cos=En@qv
+    cos=np.where(HAVE&OK,cos,-2.0)
+    order=np.argsort(-cos)
+    semfull=[(int(i),float(cos[i])) for i in order[:400]]
+    Sleg=[(i,(c-SEED_MIN)/(1-SEED_MIN)) for i,c in semfull if c>SEED_MIN]
+    semseed=[i for i,c in semfull[:SEED_K] if c>0.0]
+    # assoc
+    act={}; seen={}; qq=[]
+    for i,_,_ in L[:ASSOC_SEEDS]:
+        act[i]=1.0; seen[i]=2; qq.append((i,0))
+    for i in semseed:
+        if i in seen: continue
+        act[i]=1.0; seen[i]=2; qq.append((i,0))
+    qh=0
+    while qh<len(qq):
+        cur,h=qq[qh]; qh+=1
+        if h>=DEPTH: continue
+        parent=act[cur]
+        for e,oi in ADJ_F[cur]+ADJ_T[cur]:
+            if e['rel'] not in STRUCT: continue
+            if EXCL[oi]: continue
+            na=parent*e['w']*DECAY*SAL[oi]
+            if na<FIRE: continue
+            if seen.get(oi) and na<=act.get(oi,0): continue
+            act[oi]=na
+            if not seen.get(oi): seen[oi]=1
+            if len(qq)<AMAX*4: qq.append((oi,h+1))
+    A=[]
+    for i,st in seen.items():
+        if st!=1: continue
+        if not OK[i] or not HAVE[i]: continue
+        c=float(cos[i])
+        if c<=0.0: continue
+        A.append((i,c))
+    A.sort(key=lambda x:-x[1]); A=A[:AMAX]
+    return L,Sleg,A,cos
+def interleave3(L,Sl,A,lim=10):
+    out=[]; li=si=ai=0
+    while len(out)<lim and (li<len(L) or si<len(Sl) or ai<len(A)):
+        if li<len(L):
+            if L[li][0] not in out: out.append(L[li][0])
+            li+=1
+        if len(out)>=lim: break
+        if si<len(Sl):
+            if Sl[si][0] not in out: out.append(Sl[si][0])
+            si+=1
+        if len(out)>=lim: break
+        if ai<len(A):
+            if A[ai][0] not in out: out.append(A[ai][0])
+            ai+=1
+    return out

tools/retrieval-eval/merge-corpus.py

@@ -0,0 +1,17 @@
+import json,sys
+SRC="/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json"
+TSV,OUT=sys.argv[1],sys.argv[2]
+emb={}
+for line in open(TSV,encoding='utf-8',errors='surrogateescape'):
+    p=line.rstrip("\n").rsplit("\t",1)
+    if len(p)==2 and p[1].count(",")>100: emb[p[0]]=p[1]
+print("vectors",len(emb),flush=True)
+d=json.load(open(SRC,encoding='utf-8',errors='surrogateescape'))
+hit=0
+for n in d["nodes"]:
+    v=emb.get(n.get("id") or "")
+    if v: n["emb"]=v; hit+=1
+print("attached",hit,"of",len(d["nodes"]),flush=True)
+with open(OUT,"w",encoding='utf-8',errors='surrogateescape') as f:
+    json.dump(d,f,ensure_ascii=False)
+print("wrote",OUT,flush=True)

tools/retrieval-eval/policy2.py

@@ -0,0 +1,102 @@
+import json,sys,pickle,numpy as np
+sys.path.insert(0,'.')
+from legs import *
+GP='/Users/timlingo/Development/neuron-technologies/_wt-bm25lex/tools/retrieval-eval/'
+G=json.load(open(GP+'gold_set.json'))
+def legs3(query, sem_sal=False, assoc_sal=False, unfloor=False, sem_cap=None):
+    toks=tokenize(query)
+    hit_idx=[];hit_mask=[];df=[0]*len(toks);lt=[t.lower() for t in toks]
+    for i in range(N):
+        if not OK[i]: continue
+        s=LOW[i];m=0
+        for t,tok in enumerate(lt):
+            if tok in s: m|=(1<<t)
+        if m:
+            hit_idx.append(i);hit_mask.append(m)
+            for t in range(len(toks)):
+                if m>>t&1: df[t]+=1
+    dl_n=int(OK.sum());avgdl=float(DL[OK].sum()/max(dl_n,1))
+    idf=[math.log(1.0+((dl_n-d+0.5)/(d+0.5))) for d in df]
+    L=[]
+    for j,i in enumerate(hit_idx):
+        norm=1.0-B+B*(DL[i]/avgdl);w=0.0
+        for t in range(len(toks)):
+            if hit_mask[j]>>t&1: w+=idf[t]*(K1+1.0)/(1.0+K1*norm)
+        L.append((i,w,SAL[i]))
+    L.sort(key=lambda x:(-x[1],-x[2]))
+    if not L: return [],[],[]
+    qv=qemb(query);cos=En@qv;cos=np.where(HAVE&OK,cos,-2.0)
+    order=np.argsort(-cos)[:600]
+    cand=[int(i) for i in order if cos[i]>(0.0 if unfloor else SEED_MIN)]
+    key=(lambda i:(SAL[i] if sem_sal else 1.0)*float(cos[i]))
+    Sl=sorted(cand,key=lambda i:-key(i))
+    if sem_cap: Sl=Sl[:sem_cap]
+    semseed=[int(i) for i in order[:SEED_K] if cos[i]>0.0]
+    act={};seen={};qq=[]
+    for i,_,_ in L[:ASSOC_SEEDS]:
+        act[i]=1.0;seen[i]=2;qq.append((i,0))
+    for i in semseed:
+        if i in seen: continue
+        act[i]=1.0;seen[i]=2;qq.append((i,0))
+    qh=0
+    while qh<len(qq):
+        cur,h=qq[qh];qh+=1
+        if h>=DEPTH: continue
+        parent=act[cur]
+        for e,oi in ADJ_F[cur]+ADJ_T[cur]:
+            if e['rel'] not in STRUCT: continue
+            if EXCL[oi]: continue
+            na=parent*e['w']*DECAY*SAL[oi]
+            if na<FIRE: continue
+            if seen.get(oi) and na<=act.get(oi,0): continue
+            act[oi]=na
+            if not seen.get(oi): seen[oi]=1
+            if len(qq)<AMAX*4: qq.append((oi,h+1))
+    A=[]
+    for i,st in seen.items():
+        if st!=1 or not OK[i] or not HAVE[i]: continue
+        c=float(cos[i])
+        if c<=0.0: continue
+        A.append((i,(SAL[i] if assoc_sal else 1.0)*c))
+    A.sort(key=lambda x:-x[1]);A=[i for i,_ in A[:AMAX]]
+    return [i for i,_,_ in L],Sl,A
+def merge(L,S,A,lim=10):
+    out=[];li=si=ai=0
+    while len(out)<lim and (li<len(L) or si<len(S) or ai<len(A)):
+        if li<len(L):
+            if L[li] not in out: out.append(L[li])
+            li+=1
+        if len(out)>=lim: break
+        if si<len(S):
+            if S[si] not in out: out.append(S[si])
+            si+=1
+        if len(out)>=lim: break
+        if ai<len(A):
+            if A[ai] not in out: out.append(A[ai])
+            ai+=1
+    return out
+def outcome(q,ids):
+    c=q['category']
+    if c=='nonsense': return len(ids)==0
+    if c=='superseded':
+        a,b=q['must_outrank']
+        if a not in ids: return False
+        if b not in ids: return True
+        return ids.index(a)<ids.index(b)
+    return any(x in ids[:5] for x in q['relevant'])
+def run(**kw):
+    return {q['id']:outcome(q,[NODES[i]['id'] for i in merge(*legs3(q['query'],**kw),10)]) for q in G['queries']}
+base=run()
+print("baseline",sum(base.values()),"/38  misses:",[k for k,v in base.items() if not v])
+import itertools
+for name,kw in [
+  ('sem_sal(floored)',dict(sem_sal=True)),
+  ('unfloor',dict(unfloor=True)),
+  ('unfloor+sem_sal',dict(unfloor=True,sem_sal=True)),
+  ('assoc_sal',dict(assoc_sal=True)),
+  ('unfloor+sem_sal+assoc_sal',dict(unfloor=True,sem_sal=True,assoc_sal=True)),
+  ('sem_sal+assoc_sal(floored)',dict(sem_sal=True,assoc_sal=True)),
+]:
+    r=run(**kw)
+    g=sorted(k for k in base if r[k] and not base[k]); l=sorted(k for k in base if base[k] and not r[k])
+    print("%-28s net=%+d gains=%s losses=%s"%(name,len(g)-len(l),g,l))

tools/retrieval-eval/results-act-r2.json

@@ -0,0 +1,942 @@
+{
+ "label": "act-r2",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-act",
+ "soul_md5": "77722f5a9f49494bf735c2a4be1b5dc4",
+ "corpus": "/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json",
+ "corpus_nodes": 78768,
+ "corpus_edges": 14214,
+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7902,
+ "wall_clock_s": 121.2,
+ "child_pid": 78714,
+ "child_confirmed_dead": true,
+ "aggregate": {
+  "n_queries": 38,
+  "n_scored": 35,
+  "hit@5": 0.22857142857142856,
+  "recall@5": 0.18908730158730158,
+  "recall@10": 0.24277210884353742,
+  "precision@5": 0.06857142857142857,
+  "mrr@10": 0.24154195011337865,
+  "nonsense_clean": "2/3",
+  "superseded_outranks": "0/3",
+  "latency_ms_p50": 3237.6,
+  "latency_ms_p95": 5264.0,
+  "latency_ms_max": 5510.9,
+  "errors": 0,
+  "by_category": {
+   "associative": {
+    "n": 6,
+    "hit@5": 0.0,
+    "recall@5": 0.0,
+    "recall@10": 0.0,
+    "mrr@10": 0.0
+   },
+   "exact_rare": {
+    "n": 6,
+    "hit@5": 1.0,
+    "recall@5": 1.0,
+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "nonsense": {
+    "n": 3,
+    "clean": 2,
+    "avg_false_positives": 2.6666666666666665
+   },
+   "paraphrase": {
+    "n": 13,
+    "hit@5": 0.0,
+    "recall@5": 0.0,
+    "recall@10": 0.0,
+    "mrr@10": 0.0
+   },
+   "phrase": {
+    "n": 7,
+    "hit@5": 0.2857142857142857,
+    "recall@5": 0.0882936507936508,
+    "recall@10": 0.3567176870748299,
+    "mrr@10": 0.3505668934240363
+   },
+   "superseded": {
+    "n": 3,
+    "hit@5": 0.0,
+    "recall@5": 0.0,
+    "recall@10": 0.0,
+    "mrr@10": 0.0,
+    "outranks": 0
+   }
+  }
+ },
+ "rows": [
+  {
+   "id": "q01",
+   "category": "exact_rare",
+   "query": "unjailbreakable",
+   "returned": [
+    "mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226"
+   ],
+   "n_returned": 1,
+   "latency_ms": 476.5,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q02",
+   "category": "exact_rare",
+   "query": "engram-migrate",
+   "returned": [
+    "mem-6fdf6545-5e1a-43a9-8bdc-d2cd248146a5"
+   ],
+   "n_returned": 1,
+   "latency_ms": 708.1,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q03",
+   "category": "exact_rare",
+   "query": "cartabandonedevent",
+   "returned": [
+    "mem-1ba7c67d-85b9-4c2e-9fe2-39f8b0477091"
+   ],
+   "n_returned": 1,
+   "latency_ms": 532.0,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q04",
+   "category": "exact_rare",
+   "query": "pre-apprenticeship",
+   "returned": [
+    "mem-89c02aae-d3ca-43f9-9e5d-eb369896276c"
+   ],
+   "n_returned": 1,
+   "latency_ms": 537.5,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q05",
+   "category": "exact_rare",
+   "query": "inferencenodemanager",
+   "returned": [
+    "mem-73969486-143f-4431-b5e6-6845d1cc9848"
+   ],
+   "n_returned": 1,
+   "latency_ms": 568.7,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q06",
+   "category": "exact_rare",
+   "query": "clear-eyed",
+   "returned": [
+    "knw-c72597c5-c23d-4c08-8e9e-996dadf26a99"
+   ],
+   "n_returned": 1,
+   "latency_ms": 555.4,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q07",
+   "category": "phrase",
+   "query": "patterns not returns",
+   "returned": [
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "kn-69fd6e83-7718-4824-8d66-f49d8954e224",
+    "kn-d97920d0-1649-4223-9508-c0bb621e7fc0",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "kn-c3d9d063-8c5d-45aa-900c-550914b2ff6d",
+    "kn-f838f113-76d5-4a15-9cef-14055c4723a3",
+    "bl-76e878aa-e1fe-468c-bf9c-854097cb7e0b",
+    "art-c71aef51-026f-4d63-80e9-2a0ec0dc3865",
+    "bl-e148d23c-24e8-4122-9915-d1c11f22052f",
+    "bl-31abf75b-998f-4a4f-a6dd-8204119e0451"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1906.2,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q08",
+   "category": "phrase",
+   "query": "thirty moves",
+   "returned": [
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "bl-80720fdf-7ce7-4d28-aff8-21028d3a8cfb",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "?Z?.\f?0?]P?",
+    "?Q??m?;��`'"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1103.3,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.0625,
+   "recall@10": 0.1875,
+   "precision@5": 0.2,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q09",
+   "category": "phrase",
+   "query": "Grandma Lucas",
+   "returned": [
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325"
+   ],
+   "n_returned": 6,
+   "latency_ms": 1132.4,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.5555555555555556,
+   "recall@10": 0.5555555555555556,
+   "precision@5": 1.0,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "bl-c9adb8e5-293f-4033-99f8-0405c17ef941",
+    "bl-7e7c3fdb-4132-487f-aa70-b2cd559cb7f0",
+    "bl-7aebe936-ac55-4f35-8932-adc5224ff854",
+    "bl-9d53422d-b703-4f1d-860a-8598cb29b792",
+    "mem-34f53a9d-a131-4f82-9dbd-b9eb4a9af52e",
+    "mem-60778715-758c-4677-933d-fc39b8f94152",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf"
+   ],
+   "n_returned": 10,
+   "latency_ms": 960.8,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.1111111111111111,
+   "precision@5": 0.0,
+   "mrr@10": 0.1
+  },
+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
+   "returned": [
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+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
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+    "mem-57164d5f-baf0-4149-957a-379a4e255d1a",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
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+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
+    "kn-b2a99cd7-b379-4d9b-a996-e347a02c7bad",
+    "bl-a313d67b-dd6d-4e5b-a55a-03bc7bda17ae",
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+    "art-92e1837c-5919-42d0-bbb0-4d924d7b2864",
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+    "mem-f823e835-313f-4282-b4b3-ce527ffc2f7a",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "?Z?.\f?0?]P?",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72"
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+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "returned": [
+    "art-e495c8c5-ad95-4b64-8771-f68aa4cfcd0a",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
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+    "7774a16c-1027-4e3b-a21e-67f1f95a4acd",
+    "? ?}&?#??X\b",
+    "7?e?7???\f3?",
+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a"
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+   "mrr@10": 0.1
+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
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+    "kn-82be4e41-96c5-4da3-85c0-cee10763d975",
+    "mem-ea487cb4-ed67-44ce-8402-b56bb28468d4",
+    "bl-2694b588-a6e3-43de-861c-fa7b0ec7e7fd",
+    "bl-14883d81-f7cb-46dd-82c2-a6e6980264e5",
+    "tag-dark-theme",
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+    "? ?}&?#??X\b",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "mem-0328c3cb-4550-4ce4-9284-152e832f08f6",
+    "bl-07375bf9-a169-42cd-adb3-7d32b25982f0",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "bl-e5635b1a-c5d0-4caa-bcc8-6a726ea43685",
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+    "bl-5bb8dedf-8498-4a9b-acdc-31cc9c738f2a",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    ";??A5???"
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+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
+    "bl-d24fcce8-2b55-426f-867a-db3958a622d3",
+    "tag-phase-3",
+    "tag-project-structure",
+    "tag-anthropic-contrast",
+    "tag-voice-training",
+    "tag-ebd",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    "bl-9d53422d-b703-4f1d-860a-8598cb29b792",
+    ";??A5???",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "bl-fc893be3-e6b4-4ef6-93b0-d54ca5f89083",
+    "bl-57c5cf6b-81a5-4558-9902-5c02981fe273",
+    "tag-guilds",
+    "tag-kids",
+    "tag-coexistence",
+    "tag-cultivated-general-intelligence",
+    "? ?}&?#??X\b",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    ";??A5???",
+    "mem-cdff0c49-3ac7-4de8-89ec-92d254bd0023"
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+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "bl-bd9fb314-e9d4-4b03-aef4-534dd57a2992",
+    "bl-b019ce7a-1b21-436e-812d-032f50c6c45f",
+    "bl-e98cdd4c-01b5-459e-9036-3578cd5d975a",
+    "bl-9ce4128a-9436-4b06-82bc-8a6faafa81e0",
+    "tag-stable-diffusion",
+    ";??A5???",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
+    "mem-e321e54e-8bb3-4596-b13d-bb093d6b149d",
+    "mem-e32ba5a7-c147-4dc0-9479-b720d768eda6",
+    "mem-c7a77457-478d-4eb0-a116-67205a0066a4",
+    "bl-1b20e9bc-eb37-4907-8d63-e311fd61eab8",
+    "bl-aa762207-920d-45ab-b2a3-2f8154d7ef9b",
+    "tag-misalignment",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd"
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+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "kn-48a01973-a025-471d-950f-b93e6a426d82",
+    "mem-23d22bc1-a097-446b-8f11-8aff099e0b76",
+    "mem-6f0b2b45-90c1-4356-ac01-3daac05b09c8",
+    "mem-ce5a2ffc-ad39-4728-9ac6-76fef507d5da",
+    "project-Stripe_Elements__not_hosted_checkout__Custom_URL__DAG_bundle_pricing__Stripe_Connect_80_20_",
+    "tag-provenance",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
+    "art-e495c8c5-ad95-4b64-8771-f68aa4cfcd0a"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "kn-79056192-7de8-486c-9565-f128439a6fcb",
+    "bl-f6236350-f7b8-4f4f-a702-9eef2eb76e4b",
+    "bl-7f33f1bc-99fa-4906-889f-a42375beea20",
+    "mem-ef0091d8-1b65-431e-afa8-c6c4ee5779c9",
+    "mem-1f32f73a-952c-41bc-96dc-8b8b70d8a7c1",
+    "tag-__cultivation-metric____internal-state____dharma____evidence____novel-idea____gap-compression____values____microsoft__",
+    "? ?}&?#??X\b",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3"
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+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "knw-723551f5-1950-42a3-8b89-b6a06913cef0",
+    "tag-identity-studio",
+    "tag-finance",
+    "tag-temporal",
+    "tag-barkhausen",
+    "tag-ilogger",
+    "tag-design-first",
+    ";??A5???",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "project-Goal_setting__alignment__scoring__cadence__Attaches_to_any_imprint_",
+    "tag-performed-values",
+    "tag-turing-test",
+    "tag-sealed",
+    "tag-part-5",
+    "tag-model",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "? ?}&?#??X\b",
+    ";??A5???"
+   ],
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
+    "mem-9590ba23-bddb-43e8-a571-68a263c4c364",
+    "project-Imprint__leadership_development__feedback_frameworks__performance__presence_",
+    "bl-a9e57bb2-00a1-4867-ab59-5d9271134b50",
+    "bl-c7793c4a-7630-47fc-a462-d23059087e80",
+    "tag-gateway_platform_neuron-technologies_go_proxy_llm",
+    "tag-fornax",
+    ";??A5???",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "bl-7a13527b-3e0c-418a-9f37-88fd2152e5ce",
+    "bl-3f57bc69-7285-4f4a-a861-2de52efca058",
+    "bl-5e390b10-8753-4f25-a1a5-b5dbbb002cbf",
+    "tag-ats",
+    "tag-data-model",
+    "tag-aggregation",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    ";??A5???",
+    "? ?}&?#??X\b"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "tag-memory-model",
+    "tag-storage",
+    "tag-ga4",
+    "tag-potions",
+    "tag-resonance",
+    "tag-neuron",
+    "? ?}&?#??X\b",
+    ";??A5???",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "mem-927f41ab-8ede-4f58-acb3-995db16ac775",
+    "mem-dbe80bc2-c602-46b0-b4ea-dd222e52bcde",
+    "mem-82158b02-a180-435d-84f0-0b7ce37511b4",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "tag-upload-window",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "mem-434be7c8-88cb-4039-b79a-1da4ac4de783",
+    "mem-481c769c-68cc-45c7-bc37-c0d9778fa648",
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "bl-9d8f3c5b-4bac-41ce-8ac4-44733f99d6c8",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325"
+   ],
+   "n_returned": 10,
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+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "kn-eb1c6d99-d603-4f33-be9a-c63a178690c6",
+    "mem-a3124d5b-2f50-477f-8bb5-06879f5a496c",
+    "bl-7fa1b1a8-b80a-4f28-b162-bfe73765b4f8",
+    "mem-89c02aae-d3ca-43f9-9e5d-eb369896276c",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd"
+   ],
+   "n_returned": 10,
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+   "error": null,
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+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
+    "mem-265a7107-73b3-4410-9aff-43787d5f473b",
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+   "false_positives": 0
+  },
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+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
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+    "? ?}&?#??X\b",
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+  },
+  {
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+   "query": "is the self-improvement architecture called DARMA or DHARMA",
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+    "project-worldweaver",
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+  {
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+   "query": "how many provisional patents does Will actually have",
+   "returned": [
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+    "art-7bdaff30-5af9-4f0a-93b1-751686f9de3d",
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+  {
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+    "bl-8116da7a-b039-4e08-b8d0-c1c7861f9766",
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+    "???Ͼd??W\b?",
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+ ]
+}

tools/retrieval-eval/results-act-r3.json

@@ -0,0 +1,942 @@
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+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
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+    "tag-performed-values",
+    "tag-turing-test",
+    "tag-sealed",
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+  },
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+   "query": "cheerfulness you arrive at instead of assuming",
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+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
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+    "tag-storage",
+    "tag-ga4",
+    "tag-potions",
+    "tag-resonance",
+    "tag-neuron",
+    "? ?}&?#??X\b",
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+   "query": "Grandma Lucas stroke February 2006 goodbye window",
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+   "id": "q28",
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+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
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+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
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+    "mem-9d1bf963-1b40-4588-bdb3-0432646cc623",
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+    "? ?}&?#??X\b",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "returned": [
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+   "id": "q33",
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+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
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+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "kn-333542cb-6dab-4662-9725-bf7440d28bf7",
+    "? ?}&?#??X\b",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
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+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
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+    "ctx-e5427d7d",
+    "project-worldweaver",
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+    "? ?}&?#??X\b",
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+  {
+   "id": "q37",
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+   "query": "how many provisional patents does Will actually have",
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+    "art-7bdaff30-5af9-4f0a-93b1-751686f9de3d",
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+    "project-Imprint__discovery__objection_handling__deal_strategy__pipeline__closing_",
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+    "bl-8ef1ba6b-3fa0-4dbd-98c5-31665e5694a1",
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+    "???Ͼd??W\b?"
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+}

tools/retrieval-eval/results-assoc-leg-r2.json

@@ -0,0 +1,956 @@
+{
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+   "recall@5": 0.0,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
+    "art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
+    "kn-a31e1001-342e-4deb-a2e6-6d02d1f22dee",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "?of?7???",
+    "? ?}&?#??X\b",
+    "????7???Ջ3",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "kn-d97920d0-1649-4223-9508-c0bb621e7fc0",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e"
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+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    "7?e?7???\f3?",
+    "??o?'?B???k",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "? ?}&?#??X\b",
+    "?of?7???",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
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+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "7?e?7???\f3?",
+    "ctx-cc7f",
+    "?of?7???",
+    "ctx-4a41",
+    "imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
+    "a1000001-0000-0000-0000-000000000001",
+    "knw-729fc901-8335-44c4-9f3a-b150b4aa0915",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "ctx-175f"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
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+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "? ?}&?#??X\b",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "? ?}&?#??X\b",
+    "a708dd6e-fe73-4f2f-a21e-89daa0985487",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?"
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+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "? ?}&?#??X\b",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "ԍ????X????",
+    "??????X??2c",
+    "dR????X?-?S"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1393.5,
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+   "mrr@10": 0.5
+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???",
+    "dR????X?-?S",
+    "dz????Xƹ?i",
+    "ԍ????X????",
+    "??????X??2c",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
+    "????7???Ջ3",
+    "a1000001-0000-0000-0000-000000000001",
+    "?ǚ?7??????",
+    "mem-024598a9-ed2e-4eeb-b1e1-5410856ff132",
+    "7?e?7???\f3?",
+    "mem-ade9440f-f161-4c18-9b35-1976257e6ebb",
+    "?of?7???",
+    "ea95f600-8dfd-4c7e-b077-a93dc3cd3623"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
+    "mem-bbb126a1-b297-42bb-86be-796871829c94",
+    "mem-45022957-2d78-48aa-a714-16d6eca52e0f",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "'?T?a\"B~-?8"
+   ],
+   "n_returned": 10,
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+   "error": null,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "?ǚ?7??????",
+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "7?e?7???\f3?",
+    "ctx-bb74",
+    "??S?7???",
+    "knw-f671966c-3387-4848-abca-b5deec122e00"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "7?e?7???\f3?",
+    "mem-7b74cac0-905f-4c35-9688-fbcce105a177"
+   ],
+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.25
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc"
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+   "mrr@10": 0.2
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "54608b69-78b6-4239-b60f-b8206cfecacc",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-e0bdf5d8-d163-491f-b649-453fee8b721d",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71"
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40"
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+   "n_returned": 10,
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
+    "ctx-e5427d7d",
+    "kn-b36902cc-0b05-44ba-9aa7-800e5dea9ca9",
+    "ctx-bb74",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "kn-6f248a50-355b-47bb-aec8-e0e646a9b077",
+    "kn-5adecd7e-d6db-4576-87fe-6ef8a935cea6",
+    "bl-0fac287f-f4c0-4f15-bc4d-ff7f8a7af3ae",
+    "bl-8c2d5f51-3ccd-4c2e-848a-eb60d90a3b98"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "returned": [
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "bl-2b00aeb0-c0fa-4a9f-8f30-4207e98b3d52",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b"
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+   "precision@5": 0.4,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "? ?}&?#??X\b",
+    "4f698ae6-c40e-464e-9798-50350991a188",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71"
+   ],
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+   "recall@10": 0.2727272727272727,
+   "precision@5": 0.0,
+   "mrr@10": 0.16666666666666666
+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 750.0,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 531.1,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "?V?",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "?m?\\}Q??6??",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
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tools/retrieval-eval/results-assoc-leg.json

@@ -0,0 +1,956 @@
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+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    "7?e?7???\f3?",
+    "??o?'?B???k",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "? ?}&?#??X\b",
+    "?of?7???",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "7?e?7???\f3?",
+    "ctx-cc7f",
+    "?of?7???",
+    "ctx-4a41",
+    "imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
+    "a1000001-0000-0000-0000-000000000001",
+    "knw-729fc901-8335-44c4-9f3a-b150b4aa0915",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "ctx-175f"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
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+    "knw-23c27d3b-e0d2-43a8-a80c-0a44477ae18a",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "? ?}&?#??X\b",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "? ?}&?#??X\b",
+    "a708dd6e-fe73-4f2f-a21e-89daa0985487",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?"
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+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "? ?}&?#??X\b",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "ԍ????X????",
+    "??????X??2c",
+    "dR????X?-?S"
+   ],
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+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???",
+    "dR????X?-?S",
+    "dz????Xƹ?i",
+    "ԍ????X????",
+    "??????X??2c",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
+   ],
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+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
+    "????7???Ջ3",
+    "a1000001-0000-0000-0000-000000000001",
+    "?ǚ?7??????",
+    "mem-024598a9-ed2e-4eeb-b1e1-5410856ff132",
+    "7?e?7???\f3?",
+    "mem-ade9440f-f161-4c18-9b35-1976257e6ebb",
+    "?of?7???",
+    "ea95f600-8dfd-4c7e-b077-a93dc3cd3623"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
+    "mem-bbb126a1-b297-42bb-86be-796871829c94",
+    "mem-45022957-2d78-48aa-a714-16d6eca52e0f",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "'?T?a\"B~-?8"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "?ǚ?7??????",
+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "7?e?7???\f3?",
+    "ctx-bb74",
+    "??S?7???",
+    "knw-f671966c-3387-4848-abca-b5deec122e00"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "7?e?7???\f3?",
+    "mem-7b74cac0-905f-4c35-9688-fbcce105a177"
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc"
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+   "mrr@10": 0.2
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "54608b69-78b6-4239-b60f-b8206cfecacc",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
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+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
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+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40"
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
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+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "returned": [
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
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+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
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+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b"
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+   "mrr@10": 0.5
+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "? ?}&?#??X\b",
+    "4f698ae6-c40e-464e-9798-50350991a188",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
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+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 746.6,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 519.1,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "?V?",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "?m?\\}Q??6??",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "?m?\\}Q??6??",
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+   "false_positives": 10
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "7?e?7???\f3?",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "? ?}&?#??X\b",
+    "mem-f3b37427-b7d1-4f7e-b32c-0241a20ce8da",
+    "? ?}&?#??X\b",
+    "kn-b7e98d63-8b83-4911-b4d0-990602a7f575",
+    "?of?7???",
+    "knw-e047bb42-dc5b-4383-9e88-e508dc03abe3",
+    "? ?}&?#??X\b",
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff"
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+   "outranks": true,
+   "rank_correct": 2,
+   "rank_stale": 10
+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "? ?}&?#??X\b",
+    "12082f7e-e320-438b-bd65-083d8259748f",
+    "? ?}&?#??X\b",
+    "527ecb25-2587-47eb-8269-73be2431abd4",
+    "? ?}&?#??X\b",
+    "3cf706a1-3825-45d8-b0a9-06cae6cdf5b8",
+    "? ?}&?#??X\b",
+    "4f698ae6-c40e-464e-9798-50350991a188",
+    "? ?}&?#??X\b",
+    "be3b6036-6eca-44a7-8fdf-37b23edfdfd1"
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+  {
+   "id": "q38",
+   "category": "superseded",
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+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
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+}

tools/retrieval-eval/results-baseline-embcorpus.json

@@ -0,0 +1,945 @@
+{
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+    "ԍ????X????",
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+   "query": "the elderly relative who passed while he stayed away",
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
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+   "query": "learning is the wealth creditors cannot seize",
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+  },
+  {
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+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
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+    "? ?}&?#??X\b",
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+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "??????X??2c",
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+  {
+   "id": "q22",
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+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
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+   "id": "q23",
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+    "?ǚ?7??????",
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+  {
+   "id": "q25",
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+   "returned": [
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+    "?ǚ?7??????",
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+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q29",
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+   "query": "Sarah Bishop Dyer trailer performance",
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+    "? ?}&?#??X\b",
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+   "query": "man of the house six years old expectation",
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+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
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+   "id": "q33",
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+   "query": "flarnbistle quommetry",
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+   "n_returned": 0,
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+   "false_positives": 0
+  },
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+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
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+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
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+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "?of?7???",
+    "? ?}&?#??X\b",
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+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "7?e?7???\f3?",
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+ ]
+}

tools/retrieval-eval/results-bm25lex-r2.json

@@ -0,0 +1,959 @@
+{
+ "label": "bm25lex-r2",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-bm25lex",
+ "soul_md5": "dfbd0f8e3646212db5c60026f8ad906f",
+ "corpus": "/Users/timlingo/neuron-eval-corpora/snapshot-pre-repair-20260806-embedded.json",
+ "corpus_nodes": 78768,
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+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7894,
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+   "query": "unjailbreakable",
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+  {
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+  {
+   "id": "q04",
+   "category": "exact_rare",
+   "query": "pre-apprenticeship",
+   "returned": [
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q05",
+   "category": "exact_rare",
+   "query": "inferencenodemanager",
+   "returned": [
+    "mem-73969486-143f-4431-b5e6-6845d1cc9848",
+    "bl-c1765767-3e27-449a-8c94-10411d1eb7c0",
+    "project-Add_inference_url_config_to_Neuron_MCP__Route_summarization_gen_tasks_to_Pantheon__keep_frontier_for_complex_reasoning_"
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+  {
+   "id": "q06",
+   "category": "exact_rare",
+   "query": "clear-eyed",
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q07",
+   "category": "phrase",
+   "query": "patterns not returns",
+   "returned": [
+    "tag-patterns",
+    "mem-a4a9dfc3-e40b-49b3-b1e1-060e8be2f482",
+    "project-Imprint__system_design__ADRs__tech_strategy__integration_patterns__governance_",
+    "project-Imprint__analysis_patterns__data_storytelling__SQL__dashboards__insight_framing_",
+    "bl-79028eed-c330-4724-9402-734062d13503",
+    "bl-39dad13d-7105-4049-8224-dc3c34fdb1f3",
+    "bl-4ef4d914-da46-4e0f-be78-5219b9547e9f",
+    "bl-7e7c3fdb-4132-487f-aa70-b2cd559cb7f0",
+    "bl-1d32bd54-cf17-4a1f-b235-982d09a36f04",
+    "bl-b8af6601-a8cb-41b5-aef5-ab8a57432dd5"
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+  },
+  {
+   "id": "q08",
+   "category": "phrase",
+   "query": "thirty moves",
+   "returned": [
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+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
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+  {
+   "id": "q09",
+   "category": "phrase",
+   "query": "Grandma Lucas",
+   "returned": [
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+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
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+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
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+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "project-harmonic-framework",
+    "bl-798d135f-3987-4ccd-8de6-70ca2f358337",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "project-harmonic-framework_com",
+    "bl-680b24a9-edc3-4a9d-847a-bff0b46b568c",
+    "tag-harmonic-design",
+    "bl-92acd4eb-0452-4e8e-9f54-f8cd35170d76",
+    "tag-harmonic-framework",
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
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+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "tag-sarah",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "mem-1f32f73a-952c-41bc-96dc-8b8b70d8a7c1",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
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+    "kn-6061318f-046b-4935-907d-8eafdce14930"
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+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "bl-31abf75b-998f-4a4f-a6dd-8204119e0451",
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+    "2c56a7a9-5323-4ce4-ba09-35836ba15d54",
+    "bl-39cec462-c80c-4970-a3aa-91fe83053bde"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "returned": [
+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a",
+    "8f3abb0d-77ed-4af3-9f4d-ba62cd198886",
+    "7774a16c-1027-4e3b-a21e-67f1f95a4acd",
+    "?",
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+    "?",
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+    "?",
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+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
+    "cb070131-dfd4-4a38-91d7-22b1bde164d2",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "mem-a535f205-bc4c-4058-9171-6263c496044a",
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+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "ctx-4a41"
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+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "b1183213-d659-4759-85d7-5b1f22427fe2",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
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+    "f0eb6b13-909c-4674-91ef-23301d3abc8b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
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+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
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+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "tag-fiction",
+    "knw-8fd9836c-cc39-49df-8d61-babda626cc88",
+    "mem-8d690e9d-a7e9-4062-b2f8-e2064294e463",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "mem-ce793303-c5a5-4586-a232-a3426edd9ec7",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "mem-443bd012-fc9a-4088-b236-de5157a1ef92"
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+   "mrr@10": 0.5
+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
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+    "bl-798d135f-3987-4ccd-8de6-70ca2f358337",
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+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
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+    "1219277c-1b95-45ec-95a2-07b4a47a4d92",
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+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "a1000001-0000-0000-0000-000000000010",
+    "a1000001-0000-0000-0000-000000000009",
+    "bl-448bc514-c2f1-4520-a9b1-1f3a73678d26",
+    "a1000001-0000-0000-0000-000000000012",
+    "43098881-e044-482b-8e92-471728a8ba8b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "mem-e5cc63c0-8701-49d6-855a-e387fe087771",
+    "a1000001-0000-0000-0000-000000000001"
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+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
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+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
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+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
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+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
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+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
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+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "bl-2515d870-e35e-443b-ba20-5150bbc73fed",
+    "bl-0e8f4880-7b24-43aa-aed9-ad4d9fc73ff8",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "bl-8848929a-a23a-46bc-a2c7-fe3a3bc1cddf",
+    "bl-205141ad-b2a0-4d93-86d0-89eb0723e1bd",
+    "bl-e93858c4-7cac-4b1a-bb62-490790d4c3f3",
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+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "5a2c118a-87bd-4239-97a7-9e02c5991983",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
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+    "bl-4c5b385e-135a-4663-8521-96af0b491121",
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+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "bl-8dd70cac-866d-4ff2-b9fe-b4b3c5f094bb",
+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "a0edad47-5f77-4fc3-a546-1e85f8c68e77",
+    "a1000001-0000-0000-0000-000000000001",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "96497334-b18f-495c-9228-eeb8182bdc38",
+    "mem-024598a9-ed2e-4eeb-b1e1-5410856ff132",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea"
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+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
+    "27e1b1a4-ad0b-49d9-812f-fedf43b8aabe",
+    "knw-f9ce17a7-17fc-431f-8f23-695b670ec4fa",
+    "bl-87c93185-b2bf-40af-ae23-3c830c007abf",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "077d064f-3489-4c05-9aca-3782f96b51db",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "75e036d3-c170-4e3f-acc2-e456a6850ee2",
+    "a1000001-0000-0000-0000-000000000001"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "mem-82158b02-a180-435d-84f0-0b7ce37511b4",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "e4f27651-52c5-43fd-aff3-61d31685b3cd",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "mem-5624ec9d-62ba-4aba-8a3d-6afec6c09dd4",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "mem-833dbbcd-2400-4594-bb35-93b023049ac0",
+    "a1000001-0000-0000-0000-000000000009",
+    "mem-759e78ca-5394-4244-aa39-1c1468bc5f3e",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "bl-3f57bc69-7285-4f4a-a861-2de52efca058",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "bl-0d8c5dfa-e163-4fef-a58b-56b0d076c5a8",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "mem-b99efff0-00e6-40c8-9c5b-730330eef33b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "tag-childhood"
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+   "mrr@10": 0.2
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "3499d5da-0e9c-4de4-9bc4-8941b14e0b1f",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
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+   "precision@5": 0.4,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "54608b69-78b6-4239-b60f-b8206cfecacc",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "mem-9110798f-d0cb-4446-bc2a-14f09b6a09e2",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71"
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "tag-trailer-park-paladins",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "project-trailer-park-paladins",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
+   ],
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+   "precision@5": 0.4,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
+    "bl-0fac287f-f4c0-4f15-bc4d-ff7f8a7af3ae",
+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
+    "bl-2515d870-e35e-443b-ba20-5150bbc73fed",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "kn-b36902cc-0b05-44ba-9aa7-800e5dea9ca9",
+    "bl-bea7473c-c687-414c-9c0b-00c509a616c1",
+    "bl-fc6fcb0b-9e4b-40bf-8e88-dbfe4e27c31a",
+    "kn-6f248a50-355b-47bb-aec8-e0e646a9b077",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "mem-ab34c2f7-3243-424b-affa-25555f6cf9cc"
+   ],
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "returned": [
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "bl-2b00aeb0-c0fa-4a9f-8f30-4207e98b3d52",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "knw-723551f5-1950-42a3-8b89-b6a06913cef0",
+    "tag-hope",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
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+   "precision@5": 0.2,
+   "mrr@10": 0.25
+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "knw-729fc901-8335-44c4-9f3a-b150b4aa0915",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "knw-528dbc37-eabc-4b75-a7a5-65bf38d6018a",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "knw-473f3f24-20f6-4f39-8589-3709538eb6ac",
+    "?Z?<S???K ?",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "'?T?a\"B~-?8",
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
+   ],
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 703.0,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 492.9,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "?V?",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "?m?\\}Q??6??",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "kn-66a21179-2adc-4b19-a109-880cf4674d7d",
+    "?m?\\}Q??6??",
+    "knw-723551f5-1950-42a3-8b89-b6a06913cef0",
+    "kn-333542cb-6dab-4662-9725-bf7440d28bf7"
+   ],
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+   "error": null,
+   "clean": false,
+   "false_positives": 10
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "mem-f3b37427-b7d1-4f7e-b32c-0241a20ce8da",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "tag-__darma____cgi____patents____self-improvement____character-preservation____autonomous____architecture__",
+    "kn-b7e98d63-8b83-4911-b4d0-990602a7f575",
+    "tag-__darma____cgi____patents____self-improvement____character-preservation____autonomous____kotlin____architecture__",
+    "knw-e047bb42-dc5b-4383-9e88-e508dc03abe3",
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "mem-82b93b21-a865-410f-9ec1-fc54121d9bb5",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72"
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+   "rank_correct": 2,
+   "rank_stale": 8
+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "mem-6f0b2b45-90c1-4356-ac01-3daac05b09c8",
+    "12082f7e-e320-438b-bd65-083d8259748f",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "13705072-4515-4124-963d-083af490494f",
+    "527ecb25-2587-47eb-8269-73be2431abd4",
+    "6de314bf-5c4c-4cfc-871f-fa2e422d45e6",
+    "a1000001-0000-0000-0000-000000000002",
+    "3cf706a1-3825-45d8-b0a9-06cae6cdf5b8",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "7ac62daa-2eac-4c7a-a97e-e4203fc1b57b"
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+   "rank_correct": 8,
+   "rank_stale": null
+  },
+  {
+   "id": "q38",
+   "category": "superseded",
+   "query": "is MCP still the live integration layer",
+   "returned": [
+    "5fcba804-eb5b-48ec-82da-146b1c6bb50d",
+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
+    "bl-c8c19362-430b-4817-9cf4-9e85e0099c64",
+    "bl-c5c6571e-118f-47c7-8cbb-3ed0ebf64a51",
+    "mem-101e81b4-8097-4749-8d8d-7bb66de34517",
+    "ctx-3a55",
+    "86228228-7adf-41fb-b4c4-9ceea87953ae",
+    "4509ed62-9fb2-48b8-9038-ac569fca9604",
+    "bl-4f7b651b-6b33-449c-8a3b-cfce12ce984b",
+    "mem-3a2cf162-d93b-4f29-86f2-5066fb7fe1f5"
+   ],
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+   "error": null,
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+   "recall@5": 0.0,
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+   "outranks": false,
+   "rank_correct": null,
+   "rank_stale": 5
+  }
+ ]
+}

tools/retrieval-eval/results-bm25lex.json

@@ -0,0 +1,959 @@
+{
+ "label": "bm25lex",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-bm25lex",
+ "soul_md5": "dfbd0f8e3646212db5c60026f8ad906f",
+ "corpus": "/Users/timlingo/neuron-eval-corpora/snapshot-pre-repair-20260806-embedded.json",
+ "corpus_nodes": 78768,
+ "corpus_edges": 14214,
+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7893,
+ "wall_clock_s": 50.4,
+ "child_pid": 90325,
+ "child_confirmed_dead": true,
+ "aggregate": {
+  "n_queries": 38,
+  "n_scored": 35,
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+  "mrr@10": 0.5021428571428571,
+  "nonsense_clean": "2/3",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 1184.4,
+  "latency_ms_p95": 1620.0,
+  "latency_ms_max": 1655.4,
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+   "nonsense": {
+    "n": 3,
+    "clean": 2,
+    "avg_false_positives": 3.3333333333333335
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+   "paraphrase": {
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+   "phrase": {
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+    "outranks": 2
+   }
+  }
+ },
+ "rows": [
+  {
+   "id": "q01",
+   "category": "exact_rare",
+   "query": "unjailbreakable",
+   "returned": [
+    "mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226"
+   ],
+   "n_returned": 1,
+   "latency_ms": 287.7,
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q02",
+   "category": "exact_rare",
+   "query": "engram-migrate",
+   "returned": [
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+    "bl-ba764d70-e9d7-4f62-848f-719cb665f45e",
+    "mem-22fe5ec8-ae0d-4583-a05c-d1ef50353257",
+    "bl-b28d7256-6f74-4567-bd90-40d0ef2a6d78",
+    "project-engram",
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+    "project-engram-lang",
+    "ctx-175f",
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+    "ctx-74ed"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q03",
+   "category": "exact_rare",
+   "query": "cartabandonedevent",
+   "returned": [
+    "mem-1ba7c67d-85b9-4c2e-9fe2-39f8b0477091"
+   ],
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q04",
+   "category": "exact_rare",
+   "query": "pre-apprenticeship",
+   "returned": [
+    "mem-89c02aae-d3ca-43f9-9e5d-eb369896276c"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q05",
+   "category": "exact_rare",
+   "query": "inferencenodemanager",
+   "returned": [
+    "mem-73969486-143f-4431-b5e6-6845d1cc9848",
+    "bl-c1765767-3e27-449a-8c94-10411d1eb7c0",
+    "project-Add_inference_url_config_to_Neuron_MCP__Route_summarization_gen_tasks_to_Pantheon__keep_frontier_for_complex_reasoning_"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q06",
+   "category": "exact_rare",
+   "query": "clear-eyed",
+   "returned": [
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q07",
+   "category": "phrase",
+   "query": "patterns not returns",
+   "returned": [
+    "tag-patterns",
+    "mem-a4a9dfc3-e40b-49b3-b1e1-060e8be2f482",
+    "project-Imprint__system_design__ADRs__tech_strategy__integration_patterns__governance_",
+    "project-Imprint__analysis_patterns__data_storytelling__SQL__dashboards__insight_framing_",
+    "bl-79028eed-c330-4724-9402-734062d13503",
+    "bl-39dad13d-7105-4049-8224-dc3c34fdb1f3",
+    "bl-4ef4d914-da46-4e0f-be78-5219b9547e9f",
+    "bl-7e7c3fdb-4132-487f-aa70-b2cd559cb7f0",
+    "bl-1d32bd54-cf17-4a1f-b235-982d09a36f04",
+    "bl-b8af6601-a8cb-41b5-aef5-ab8a57432dd5"
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+   "mrr@10": 0.5
+  },
+  {
+   "id": "q08",
+   "category": "phrase",
+   "query": "thirty moves",
+   "returned": [
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+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
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+  },
+  {
+   "id": "q09",
+   "category": "phrase",
+   "query": "Grandma Lucas",
+   "returned": [
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+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
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+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
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+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "project-harmonic-framework",
+    "bl-798d135f-3987-4ccd-8de6-70ca2f358337",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "project-harmonic-framework_com",
+    "bl-680b24a9-edc3-4a9d-847a-bff0b46b568c",
+    "tag-harmonic-design",
+    "bl-92acd4eb-0452-4e8e-9f54-f8cd35170d76",
+    "tag-harmonic-framework",
+    "bl-18a9d1e4-1484-474c-bf6b-c6173212181b"
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
+   "returned": [
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+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "tag-sarah",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "mem-1f32f73a-952c-41bc-96dc-8b8b70d8a7c1",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "mem-a6cb3b8d-d89c-46fc-931d-e90c560783b0",
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "bl-31abf75b-998f-4a4f-a6dd-8204119e0451",
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+    "bl-6f99e111-7055-4635-9831-a489747ce418",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
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+    "bl-8b58d9bc-352b-4842-a7f8-a6254b5d1e25",
+    "2c56a7a9-5323-4ce4-ba09-35836ba15d54",
+    "bl-39cec462-c80c-4970-a3aa-91fe83053bde"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "returned": [
+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a",
+    "8f3abb0d-77ed-4af3-9f4d-ba62cd198886",
+    "7774a16c-1027-4e3b-a21e-67f1f95a4acd",
+    "?",
+    "bl-ec84b63d-b278-4944-8d7f-4aa7a51c0315",
+    "?",
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+    "?",
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+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
+    "cb070131-dfd4-4a38-91d7-22b1bde164d2",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+    "66c63082-b4da-4aa1-8fee-848db8a83210",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "mem-a535f205-bc4c-4058-9171-6263c496044a",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "ctx-4a41"
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+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "b1183213-d659-4759-85d7-5b1f22427fe2",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "mem-16efddd1-c43d-4a42-9d78-f54fb82bd277",
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+    "f0eb6b13-909c-4674-91ef-23301d3abc8b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
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+    "54608b69-78b6-4239-b60f-b8206cfecacc",
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+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
+    "mem-ef878e30-5851-4e82-8588-745415108941",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "tag-fiction",
+    "knw-8fd9836c-cc39-49df-8d61-babda626cc88",
+    "mem-8d690e9d-a7e9-4062-b2f8-e2064294e463",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "mem-ce793303-c5a5-4586-a232-a3426edd9ec7",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "mem-443bd012-fc9a-4088-b236-de5157a1ef92"
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "bl-8de20bcf-7149-4f48-b67c-e7f9758fd6e5",
+    "bl-798d135f-3987-4ccd-8de6-70ca2f358337",
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+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "bl-164b520b-c503-49db-89f9-bd2fdf4215f5",
+    "knw-f6ed7d00-bf7d-42ce-9e40-77cf3406e918",
+    "1219277c-1b95-45ec-95a2-07b4a47a4d92",
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+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "a1000001-0000-0000-0000-000000000010",
+    "a1000001-0000-0000-0000-000000000009",
+    "bl-448bc514-c2f1-4520-a9b1-1f3a73678d26",
+    "a1000001-0000-0000-0000-000000000012",
+    "43098881-e044-482b-8e92-471728a8ba8b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "mem-e5cc63c0-8701-49d6-855a-e387fe087771",
+    "a1000001-0000-0000-0000-000000000001"
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+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
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+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
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+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "mem-cde58b77-50d3-4bac-9581-e70a4c02c015",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
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+    "mem-8d699e2c-ac2a-4742-bb62-b6da00f4b10e",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
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+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
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+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "bl-2515d870-e35e-443b-ba20-5150bbc73fed",
+    "bl-0e8f4880-7b24-43aa-aed9-ad4d9fc73ff8",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "bl-8848929a-a23a-46bc-a2c7-fe3a3bc1cddf",
+    "bl-205141ad-b2a0-4d93-86d0-89eb0723e1bd",
+    "bl-e93858c4-7cac-4b1a-bb62-490790d4c3f3",
+    "bl-34f51ddb-a840-459f-a248-94214f5febb6",
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+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
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+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
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+  },
+  {
+   "id": "q23",
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+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
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+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
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+    "96497334-b18f-495c-9228-eeb8182bdc38",
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+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
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+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
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+    "27e1b1a4-ad0b-49d9-812f-fedf43b8aabe",
+    "knw-f9ce17a7-17fc-431f-8f23-695b670ec4fa",
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+  },
+  {
+   "id": "q25",
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+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "mem-82158b02-a180-435d-84f0-0b7ce37511b4",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "e4f27651-52c5-43fd-aff3-61d31685b3cd",
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+    "mem-833dbbcd-2400-4594-bb35-93b023049ac0",
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+  },
+  {
+   "id": "q26",
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+   "query": "a childhood offering no solid foundation to inherit",
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+    "bl-3f57bc69-7285-4f4a-a861-2de52efca058",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
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+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "tag-childhood"
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+   "mrr@10": 0.2
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
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+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
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+   "mrr@10": 0.5
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "54608b69-78b6-4239-b60f-b8206cfecacc",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "mem-9110798f-d0cb-4446-bc2a-14f09b6a09e2",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71"
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "tag-trailer-park-paladins",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "project-trailer-park-paladins",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
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+   "precision@5": 0.4,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
+    "bl-0fac287f-f4c0-4f15-bc4d-ff7f8a7af3ae",
+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
+    "bl-2515d870-e35e-443b-ba20-5150bbc73fed",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "kn-b36902cc-0b05-44ba-9aa7-800e5dea9ca9",
+    "bl-bea7473c-c687-414c-9c0b-00c509a616c1",
+    "bl-fc6fcb0b-9e4b-40bf-8e88-dbfe4e27c31a",
+    "kn-6f248a50-355b-47bb-aec8-e0e646a9b077",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "mem-ab34c2f7-3243-424b-affa-25555f6cf9cc"
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "returned": [
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "bl-2b00aeb0-c0fa-4a9f-8f30-4207e98b3d52",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "knw-723551f5-1950-42a3-8b89-b6a06913cef0",
+    "tag-hope",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
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+   "precision@5": 0.2,
+   "mrr@10": 0.25
+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "knw-729fc901-8335-44c4-9f3a-b150b4aa0915",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "knw-528dbc37-eabc-4b75-a7a5-65bf38d6018a",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "knw-473f3f24-20f6-4f39-8589-3709538eb6ac",
+    "?Z?<S???K ?",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "'?T?a\"B~-?8",
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
+   ],
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 703.8,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 488.0,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "?V?",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "?m?\\}Q??6??",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "kn-66a21179-2adc-4b19-a109-880cf4674d7d",
+    "?m?\\}Q??6??",
+    "knw-723551f5-1950-42a3-8b89-b6a06913cef0",
+    "kn-333542cb-6dab-4662-9725-bf7440d28bf7"
+   ],
+   "n_returned": 10,
+   "latency_ms": 720.7,
+   "error": null,
+   "clean": false,
+   "false_positives": 10
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "mem-f3b37427-b7d1-4f7e-b32c-0241a20ce8da",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "tag-__darma____cgi____patents____self-improvement____character-preservation____autonomous____architecture__",
+    "kn-b7e98d63-8b83-4911-b4d0-990602a7f575",
+    "tag-__darma____cgi____patents____self-improvement____character-preservation____autonomous____kotlin____architecture__",
+    "knw-e047bb42-dc5b-4383-9e88-e508dc03abe3",
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "mem-82b93b21-a865-410f-9ec1-fc54121d9bb5",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72"
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+   "outranks": true,
+   "rank_correct": 2,
+   "rank_stale": 8
+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "mem-6f0b2b45-90c1-4356-ac01-3daac05b09c8",
+    "12082f7e-e320-438b-bd65-083d8259748f",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "13705072-4515-4124-963d-083af490494f",
+    "527ecb25-2587-47eb-8269-73be2431abd4",
+    "6de314bf-5c4c-4cfc-871f-fa2e422d45e6",
+    "a1000001-0000-0000-0000-000000000002",
+    "3cf706a1-3825-45d8-b0a9-06cae6cdf5b8",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "7ac62daa-2eac-4c7a-a97e-e4203fc1b57b"
+   ],
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+   "rank_correct": 8,
+   "rank_stale": null
+  },
+  {
+   "id": "q38",
+   "category": "superseded",
+   "query": "is MCP still the live integration layer",
+   "returned": [
+    "5fcba804-eb5b-48ec-82da-146b1c6bb50d",
+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
+    "bl-c8c19362-430b-4817-9cf4-9e85e0099c64",
+    "bl-c5c6571e-118f-47c7-8cbb-3ed0ebf64a51",
+    "mem-101e81b4-8097-4749-8d8d-7bb66de34517",
+    "ctx-3a55",
+    "86228228-7adf-41fb-b4c4-9ceea87953ae",
+    "4509ed62-9fb2-48b8-9038-ac569fca9604",
+    "bl-4f7b651b-6b33-449c-8a3b-cfce12ce984b",
+    "mem-3a2cf162-d93b-4f29-86f2-5066fb7fe1f5"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1021.6,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
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+   "outranks": false,
+   "rank_correct": null,
+   "rank_stale": 5
+  }
+ ]
+}

tools/retrieval-eval/results-feat-recall-through-activation.json

@@ -0,0 +1,942 @@
+{
+ "label": "act-r1",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-act",
+ "soul_md5": "77722f5a9f49494bf735c2a4be1b5dc4",
+ "corpus": "/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json",
+ "corpus_nodes": 78768,
+ "corpus_edges": 14214,
+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7894,
+ "wall_clock_s": 112.3,
+ "child_pid": 78648,
+ "child_confirmed_dead": true,
+ "aggregate": {
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+  "precision@5": 0.07428571428571429,
+  "mrr@10": 0.24154195011337865,
+  "nonsense_clean": "2/3",
+  "superseded_outranks": "0/3",
+  "latency_ms_p50": 3208.8,
+  "latency_ms_p95": 4851.9,
+  "latency_ms_max": 5078.8,
+  "errors": 0,
+  "by_category": {
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+    "mrr@10": 1.0
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+    "? ?}&?#??X\b",
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+   "query": "Directed Autonomous Runtime Modification",
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+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "?Z?.\f?0?]P?",
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+    "? ?}&?#??X\b",
+    "7?e?7???\f3?",
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+   "query": "the elderly relative who passed while he stayed away",
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+    "? ?}&?#??X\b",
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+   "query": "a soldier sidelined by illness who refused to quit",
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+    "bl-07375bf9-a169-42cd-adb3-7d32b25982f0",
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+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    "015644f5-8194-4af0-800d-dd4a0cd71396"
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+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
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+    "bl-fc893be3-e6b4-4ef6-93b0-d54ca5f89083",
+    "tag-project-structure",
+    "tag-anthropic-contrast",
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+    "015644f5-8194-4af0-800d-dd4a0cd71396",
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+  {
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+   "query": "a tight payload beats a bloated one",
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+    "tag-phase-3",
+    "tag-identity-studio",
+    "tag-kids",
+    "tag-coexistence",
+    "tag-cultivated-general-intelligence",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "? ?}&?#??X\b",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "mem-cdff0c49-3ac7-4de8-89ec-92d254bd0023"
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+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
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+    "bl-bd9fb314-e9d4-4b03-aef4-534dd57a2992",
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+    "bl-e98cdd4c-01b5-459e-9036-3578cd5d975a",
+    "bl-9ce4128a-9436-4b06-82bc-8a6faafa81e0",
+    "tag-stable-diffusion",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
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+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
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+    "mem-e32ba5a7-c147-4dc0-9479-b720d768eda6",
+    "mem-c7a77457-478d-4eb0-a116-67205a0066a4",
+    "bl-1b20e9bc-eb37-4907-8d63-e311fd61eab8",
+    "bl-aa762207-920d-45ab-b2a3-2f8154d7ef9b",
+    "tag-misalignment",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "? ?}&?#??X\b",
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+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
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+    "bl-7f33f1bc-99fa-4906-889f-a42375beea20",
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+    "mem-ce5a2ffc-ad39-4728-9ac6-76fef507d5da",
+    "project-Stripe_Elements__not_hosted_checkout__Custom_URL__DAG_bundle_pricing__Stripe_Connect_80_20_",
+    "tag-provenance",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
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+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
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+    "bl-f6236350-f7b8-4f4f-a702-9eef2eb76e4b",
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+    "tag-__cultivation-metric____internal-state____dharma____evidence____novel-idea____gap-compression____values____microsoft__",
+    "? ?}&?#??X\b",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
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+   "id": "q23",
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+   "query": "a mind that compounds instead of resetting each day",
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+    "tag-turing-test",
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+  },
+  {
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+  },
+  {
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+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
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+    "tag-storage",
+    "tag-ga4",
+    "tag-potions",
+    "tag-resonance",
+    "tag-neuron",
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+  },
+  {
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+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "tag-upload-window",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
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+  },
+  {
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+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
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+  },
+  {
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+   "query": "Sarah Bishop Dyer trailer performance",
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+    "project-Imprint__leadership_development__feedback_frameworks__performance__presence_",
+    "mem-5e7f6ddd-c818-4ad3-b564-54ae278e9976",
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+    "mem-89c02aae-d3ca-43f9-9e5d-eb369896276c",
+    "tag-sarah",
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+    "? ?}&?#??X\b",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
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+    "mem-9d1bf963-1b40-4588-bdb3-0432646cc623",
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+    "tag-__patents____swarm____claim-language____prior-art____filing__",
+    "? ?}&?#??X\b",
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+   "query": "hope won inside the narrative preface",
+   "returned": [
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+    "bl-e148d23c-24e8-4122-9915-d1c11f22052f",
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+  },
+  {
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+   "query": "man of the house six years old expectation",
+   "returned": [
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+    "bl-ffa22d7e-42a9-4bd2-a428-1d2df243ac93",
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+    "bl-4a6746e8-191f-48fc-8bfb-c4dc73b80bcd",
+    "tag-command-pattern",
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+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
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+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 1342.7,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 874.8,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "kn-333542cb-6dab-4662-9725-bf7440d28bf7",
+    "? ?}&?#??X\b",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
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+   "error": null,
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+   "false_positives": 8
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
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+    "project-worldweaver",
+    "tag-__kotlin____internal-state____pre-reasoning____post-reasoning____compression-ratio____dharma____cultivation__",
+    "tag-import",
+    "tag-enterprise",
+    "tag-__cgi____dharma____cultivation____five-primitives____seed-artifact____agi____intelligence____whitepaper____patent__",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f",
+    "? ?}&?#??X\b",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "015644f5-8194-4af0-800d-dd4a0cd71396"
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+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "mem-bfe0fafd-2750-4fdc-b773-04e878b3b23f",
+    "art-7bdaff30-5af9-4f0a-93b1-751686f9de3d",
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+    "mem-32203649-3213-4d6d-86fd-3d657ac70d77",
+    "mem-22f5f665-3ad2-4063-88b0-915849a795f5",
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+  {
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+    "bl-8116da7a-b039-4e08-b8d0-c1c7861f9766",
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+    "tag-dark-theme",
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+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "???Ͼd??W\b?"
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+  }
+ ]
+}

tools/retrieval-eval/results-hybrid-r2.json

@@ -0,0 +1,956 @@
+{
+ "label": "hybrid-semantic-r2",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-hybrid",
+ "soul_md5": "5cd2718932c2ecf4940ddfe5a9c8abbe",
+ "corpus": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/corpus-embedded.json",
+ "corpus_nodes": 78768,
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+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7895,
+ "wall_clock_s": 52.1,
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+ "rows": [
+  {
+   "id": "q01",
+   "category": "exact_rare",
+   "query": "unjailbreakable",
+   "returned": [
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q02",
+   "category": "exact_rare",
+   "query": "engram-migrate",
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+    "mem-22fe5ec8-ae0d-4583-a05c-d1ef50353257",
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+    "project-engram-lang",
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+  {
+   "id": "q03",
+   "category": "exact_rare",
+   "query": "cartabandonedevent",
+   "returned": [
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+  {
+   "id": "q04",
+   "category": "exact_rare",
+   "query": "pre-apprenticeship",
+   "returned": [
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+  },
+  {
+   "id": "q05",
+   "category": "exact_rare",
+   "query": "inferencenodemanager",
+   "returned": [
+    "mem-73969486-143f-4431-b5e6-6845d1cc9848",
+    "bl-c1765767-3e27-449a-8c94-10411d1eb7c0",
+    "project-Add_inference_url_config_to_Neuron_MCP__Route_summarization_gen_tasks_to_Pantheon__keep_frontier_for_complex_reasoning_"
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+   "id": "q06",
+   "category": "exact_rare",
+   "query": "clear-eyed",
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+  },
+  {
+   "id": "q07",
+   "category": "phrase",
+   "query": "patterns not returns",
+   "returned": [
+    "mem-a4a9dfc3-e40b-49b3-b1e1-060e8be2f482",
+    "????7???Ջ3",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
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+   "id": "q08",
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+   "id": "q09",
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+   "query": "Grandma Lucas",
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+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
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+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "ԍ????X????",
+    "project-harmonic-framework",
+    "?ǚ?7??????",
+    "project-harmonic-framework_com",
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "??????X??2c",
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+    "????7???Ջ3",
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+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
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+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
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+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
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+   "id": "q12",
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+   "query": "Directed Autonomous Runtime Modification",
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+    "? ?}&?#??X\b"
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+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
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+    "8f3abb0d-77ed-4af3-9f4d-ba62cd198886",
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+    "?",
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+    "?",
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+   "query": "the elderly relative who passed while he stayed away",
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+   "query": "a soldier sidelined by illness who refused to quit",
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+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+    "kn-a31e1001-342e-4deb-a2e6-6d02d1f22dee",
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+  {
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+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
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+    "7?e?7???\f3?",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
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+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    "7?e?7???\f3?",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "??o?'?B???k",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
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+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
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+    "7?e?7???\f3?",
+    "?of?7???",
+    "imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
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+    "kn-83bb86c6-521d-416c-a86e-6e29c2d8f102",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
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+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
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+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
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+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "7?e?7???\f3?",
+    "kn-0625e393-067c-4bba-8389-7e1b79265142",
+    "??o?'?B???k",
+    "kn-150e6790-fc2a-48a7-8289-313c1fbaf5ae",
+    "? ?}&?#??X\b"
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+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "? ?}&?#??X\b",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
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+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?"
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+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "? ?}&?#??X\b",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "ԍ????X????",
+    "??????X??2c",
+    "dR????X?-?S"
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+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "?of?7???",
+    "??????X??2c",
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+    "ԍ????X????",
+    "dR????X?-?S",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
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+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
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+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
+    "????7???Ջ3",
+    "a1000001-0000-0000-0000-000000000001",
+    "?ǚ?7??????",
+    "mem-024598a9-ed2e-4eeb-b1e1-5410856ff132",
+    "7?e?7???\f3?",
+    "mem-ade9440f-f161-4c18-9b35-1976257e6ebb",
+    "?of?7???",
+    "ea95f600-8dfd-4c7e-b077-a93dc3cd3623"
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+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
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+    "mem-45022957-2d78-48aa-a714-16d6eca52e0f",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "'?T?a\"B~-?8"
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+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "?ǚ?7??????",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
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+    "??S?7???",
+    "??f?7???",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
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+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "7?e?7???\f3?",
+    "mem-7b74cac0-905f-4c35-9688-fbcce105a177"
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+   "precision@5": 0.2,
+   "mrr@10": 0.25
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
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+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "art-e0bdf5d8-d163-491f-b649-453fee8b721d",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q29",
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+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "7?e?7???\f3?",
+    "?of?7???",
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+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
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+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
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+    "bl-8c2d5f51-3ccd-4c2e-848a-eb60d90a3b98",
+    "7?e?7???\f3?",
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+   "id": "q31",
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+   "query": "hope won inside the narrative preface",
+   "returned": [
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+    "bl-2b00aeb0-c0fa-4a9f-8f30-4207e98b3d52",
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+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "7?e?7???\f3?",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
+    "rQ??m?;?x?'"
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+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
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+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 519.6,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "?V?",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "?m?\\}Q??6??",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "?m?\\}Q??6??",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "?m?\\}Q??6??",
+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "?m?\\}Q??6??"
+   ],
+   "n_returned": 10,
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+   "error": null,
+   "clean": false,
+   "false_positives": 10
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "7?e?7???\f3?",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "? ?}&?#??X\b",
+    "mem-f3b37427-b7d1-4f7e-b32c-0241a20ce8da",
+    "? ?}&?#??X\b",
+    "kn-b7e98d63-8b83-4911-b4d0-990602a7f575",
+    "?of?7???",
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+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "? ?}&?#??X\b",
+    "12082f7e-e320-438b-bd65-083d8259748f",
+    "? ?}&?#??X\b",
+    "527ecb25-2587-47eb-8269-73be2431abd4",
+    "? ?}&?#??X\b",
+    "3cf706a1-3825-45d8-b0a9-06cae6cdf5b8",
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+    "4f698ae6-c40e-464e-9798-50350991a188",
+    "? ?}&?#??X\b",
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+  {
+   "id": "q38",
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+   "query": "is MCP still the live integration layer",
+   "returned": [
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+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
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+    "mem-101e81b4-8097-4749-8d8d-7bb66de34517",
+    "? ?}&?#??X\b",
+    "4509ed62-9fb2-48b8-9038-ac569fca9604",
+    "%???2??jH??",
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+    "???Ͼd??W\b?",
+    "bl-556438af-57b2-4bd8-a747-9f868aaee290"
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+ ]
+}

tools/retrieval-eval/results-hybrid.json

@@ -0,0 +1,956 @@
+{
+ "label": "hybrid-semantic",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-hybrid",
+ "soul_md5": "5cd2718932c2ecf4940ddfe5a9c8abbe",
+ "corpus": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/corpus-embedded.json",
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+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
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+ "rows": [
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+   "query": "unjailbreakable",
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+    "mem-22fe5ec8-ae0d-4583-a05c-d1ef50353257",
+    "project-engram",
+    "project-engram-lang",
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+    "bl-c1765767-3e27-449a-8c94-10411d1eb7c0",
+    "project-Add_inference_url_config_to_Neuron_MCP__Route_summarization_gen_tasks_to_Pantheon__keep_frontier_for_complex_reasoning_"
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+  },
+  {
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+   "query": "patterns not returns",
+   "returned": [
+    "mem-a4a9dfc3-e40b-49b3-b1e1-060e8be2f482",
+    "????7???Ջ3",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
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+  },
+  {
+   "id": "q08",
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+   "query": "thirty moves",
+   "returned": [
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "Z[?<S???H??",
+    "rQ??m?;?x?'",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
+   ],
+   "n_returned": 10,
+   "latency_ms": 543.5,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.3125,
+   "recall@10": 0.5,
+   "precision@5": 1.0,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q09",
+   "category": "phrase",
+   "query": "Grandma Lucas",
+   "returned": [
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325"
+   ],
+   "n_returned": 10,
+   "latency_ms": 547.8,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.3333333333333333,
+   "recall@10": 0.5555555555555556,
+   "precision@5": 0.6,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "ԍ????X????",
+    "project-harmonic-framework",
+    "?ǚ?7??????",
+    "project-harmonic-framework_com",
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "??????X??2c",
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "????7???Ջ3",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356"
+   ],
+   "n_returned": 10,
+   "latency_ms": 518.8,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.1111111111111111,
+   "precision@5": 0.0,
+   "mrr@10": 0.1111111111111111
+  },
+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "mem-a9a9ce95-0d64-46eb-9db8-ff81d78ade35",
+    "mem-b8ecd23e-77ce-42f7-984c-f51453fec16d"
+   ],
+   "n_returned": 10,
+   "latency_ms": 534.2,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.5,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.2
+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
+    "mem-82b93b21-a865-410f-9ec1-fc54121d9bb5",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?",
+    "?of?7???",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 9,
+   "latency_ms": 895.5,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.2857142857142857,
+   "recall@10": 0.5,
+   "precision@5": 0.8,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "returned": [
+    "7774a16c-1027-4e3b-a21e-67f1f95a4acd",
+    "8f3abb0d-77ed-4af3-9f4d-ba62cd198886",
+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a",
+    "?",
+    "mem-dba009a2-d2ea-4f5a-b9e8-0f04bc9ab32f",
+    "?",
+    "mem-7cd90611-88a3-423d-a38a-0db2812952fa",
+    "?",
+    "bl-07375bf9-a169-42cd-adb3-7d32b25982f0",
+    "?"
+   ],
+   "n_returned": 10,
+   "latency_ms": 763.0,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.3333333333333333
+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "????7???Ջ3",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1650.1,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
+    "art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
+    "kn-a31e1001-342e-4deb-a2e6-6d02d1f22dee",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1720.2,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "?of?7???",
+    "? ?}&?#??X\b",
+    "????7???Ջ3",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "kn-d97920d0-1649-4223-9508-c0bb621e7fc0",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1396.3,
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+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    "7?e?7???\f3?",
+    "??o?'?B???k",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "? ?}&?#??X\b",
+    "?of?7???",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1126.6,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "7?e?7???\f3?",
+    "?of?7???",
+    "imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "kn-c2205725-69d0-4dd1-9a8d-1c7fa9a0c7b4",
+    "kn-83bb86c6-521d-416c-a86e-6e29c2d8f102",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 9,
+   "latency_ms": 1452.3,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "7?e?7???\f3?",
+    "kn-0625e393-067c-4bba-8389-7e1b79265142",
+    "??o?'?B???k",
+    "kn-150e6790-fc2a-48a7-8289-313c1fbaf5ae",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1303.1,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "? ?}&?#??X\b",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "? ?}&?#??X\b",
+    "a708dd6e-fe73-4f2f-a21e-89daa0985487",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1618.6,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "? ?}&?#??X\b",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "ԍ????X????",
+    "??????X??2c",
+    "dR????X?-?S"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1406.9,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???",
+    "dR????X?-?S",
+    "dz????Xƹ?i",
+    "ԍ????X????",
+    "??????X??2c",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1667.1,
+   "error": null,
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+   "recall@5": 0.0,
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
+    "????7???Ջ3",
+    "a1000001-0000-0000-0000-000000000001",
+    "?ǚ?7??????",
+    "mem-024598a9-ed2e-4eeb-b1e1-5410856ff132",
+    "7?e?7???\f3?",
+    "mem-ade9440f-f161-4c18-9b35-1976257e6ebb",
+    "?of?7???",
+    "ea95f600-8dfd-4c7e-b077-a93dc3cd3623"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1528.6,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
+    "mem-bbb126a1-b297-42bb-86be-796871829c94",
+    "mem-45022957-2d78-48aa-a714-16d6eca52e0f",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "'?T?a\"B~-?8"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1579.9,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "?ǚ?7??????",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "7?e?7???\f3?",
+    "??S?7???",
+    "??f?7???",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "??S?7???",
+    "??S?7???",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1288.7,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "7?e?7???\f3?",
+    "mem-7b74cac0-905f-4c35-9688-fbcce105a177"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1383.8,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.25
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "?ǚ?7??????"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1499.4,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "art-e0bdf5d8-d163-491f-b649-453fee8b721d",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???"
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+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "7?e?7???\f3?",
+    "?of?7???",
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+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
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+   "query": "hope won inside the narrative preface",
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+  },
+  {
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+   "query": "man of the house six years old expectation",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
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+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 525.1,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "?V?",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "?m?\\}Q??6??",
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+    "?m?\\}Q??6??",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "?m?\\}Q??6??",
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+    "?m?\\}Q??6??"
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+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "7?e?7???\f3?",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "? ?}&?#??X\b",
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+    "? ?}&?#??X\b",
+    "kn-b7e98d63-8b83-4911-b4d0-990602a7f575",
+    "?of?7???",
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+    "? ?}&?#??X\b",
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+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "? ?}&?#??X\b",
+    "12082f7e-e320-438b-bd65-083d8259748f",
+    "? ?}&?#??X\b",
+    "527ecb25-2587-47eb-8269-73be2431abd4",
+    "? ?}&?#??X\b",
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+    "4f698ae6-c40e-464e-9798-50350991a188",
+    "? ?}&?#??X\b",
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+  {
+   "id": "q38",
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+   "returned": [
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+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
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+    "mem-101e81b4-8097-4749-8d8d-7bb66de34517",
+    "? ?}&?#??X\b",
+    "4509ed62-9fb2-48b8-9038-ac569fca9604",
+    "%???2??jH??",
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+    "???Ͼd??W\b?",
+    "bl-556438af-57b2-4bd8-a747-9f868aaee290"
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+ ]
+}

tools/retrieval-eval/results-main-r2.json

@@ -0,0 +1,945 @@
+{
+ "label": "main-r2",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-main",
+ "soul_md5": "caf822425540114984bfcd713ad37162",
+ "corpus": "/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json",
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+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7895,
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+ "rows": [
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+  {
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+   "query": "cartabandonedevent",
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+    "?ǚ?7??????",
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+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
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+   "id": "q09",
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+   "query": "Grandma Lucas",
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+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
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+    "ԍ????X????",
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "?ǚ?7??????",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "????7???Ջ3",
+    "??????X??2c",
+    "g?e?7???'c?"
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+  {
+   "id": "q11",
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+   "query": "Sarah Bishop",
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+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "mem-a9a9ce95-0d64-46eb-9db8-ff81d78ade35",
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+   "mrr@10": 0.2
+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
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+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
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+    "? ?}&?#??X\b"
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+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
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+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a",
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+    "7?e?7???\f3?",
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+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
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+   "id": "q15",
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+   "query": "a soldier sidelined by illness who refused to quit",
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+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
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+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
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+   "id": "q17",
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+    "7?e?7???\f3?",
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+    "? ?}&?#??X\b",
+    "??o?'?B???k",
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+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "7?e?7???\f3?",
+    "?of?7???",
+    "imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
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+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
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+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
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+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
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+    "? ?}&?#??X\b",
+    "kn-0625e393-067c-4bba-8389-7e1b79265142",
+    "ע?RGk?\tH(?"
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+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?",
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+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "??????X??2c",
+    "ԍ????X????",
+    "dR????X?-?S",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "dz????Xƹ?i",
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+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "dR????X?-?S",
+    "dz????Xƹ?i",
+    "ԍ????X????",
+    "??????X??2c",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
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+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "?ǚ?7??????",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "????7???Ջ3",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "%???2??jH??",
+    "? ?}&?#??X\b",
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+    "?of?7???"
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+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
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+    "mem-45022957-2d78-48aa-a714-16d6eca52e0f",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "'?T?a\"B~-?8"
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+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "?ǚ?7??????",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "7?e?7???\f3?",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "??S?7???",
+    "? ?}&?#??X\b",
+    "??f?7???",
+    "??S?7???",
+    "knw-5578cb21-e899-4822-b7f4-0d96fa094e3d"
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+   "n_returned": 10,
+   "latency_ms": 1192.2,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "? ?}&?#??X\b",
+    "??o?'?B???k",
+    "?of?7???",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "?ǚ?7??????"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1448.6,
+   "error": null,
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+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "art-e0bdf5d8-d163-491f-b649-453fee8b721d",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???"
+   ],
+   "n_returned": 10,
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+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "7?e?7???\f3?",
+    "?of?7???",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "bl-0fac287f-f4c0-4f15-bc4d-ff7f8a7af3ae",
+    "7?e?7???\f3?",
+    "kn-6f248a50-355b-47bb-aec8-e0e646a9b077",
+    "? ?}&?#??X\b",
+    "h??I?cB?Q??",
+    "?of?7???",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1154.5,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "returned": [
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "7?e?7???\f3?",
+    "rQ??m?;?x?'",
+    "?Q??m?;?u?'",
+    "R^??m?;��?'",
+    "?Q??m?;��`'",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 9,
+   "latency_ms": 1187.5,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef"
+   ],
+   "n_returned": 10,
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+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 684.0,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 444.0,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+}

tools/retrieval-eval/results-main-r3.json

@@ -0,0 +1,945 @@
+{
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+   "query": "choosing an uncomfortable fact over a pleasant fiction",
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+    "?of?7???",
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+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
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+   "id": "q19",
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+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
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+    "ע?RGk?\tH(?"
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+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?",
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+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "??????X??2c",
+    "ԍ????X????",
+    "dR????X?-?S",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "dz????Xƹ?i",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "dR????X?-?S",
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+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
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+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "????7???Ջ3",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "?ǚ?7??????",
+    "7?e?7???\f3?",
+    "??f?7???",
+    "? ?}&?#??X\b",
+    "%???2??jH??",
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+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
+    "mem-bbb126a1-b297-42bb-86be-796871829c94",
+    "mem-45022957-2d78-48aa-a714-16d6eca52e0f",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
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+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "'?T?a\"B~-?8"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "?ǚ?7??????",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "7?e?7???\f3?",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "??S?7???",
+    "? ?}&?#??X\b",
+    "??f?7???",
+    "??S?7???",
+    "knw-5578cb21-e899-4822-b7f4-0d96fa094e3d"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "? ?}&?#??X\b",
+    "??o?'?B???k",
+    "?of?7???",
+    "? ?}&?#??X\b"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "?ǚ?7??????"
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+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+    "art-e0bdf5d8-d163-491f-b649-453fee8b721d",
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+    "? ?}&?#??X\b",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
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+    "?of?7???",
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+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
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+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
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+    "? ?}&?#??X\b",
+    "h??I?cB?Q??",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "returned": [
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "7?e?7???\f3?",
+    "rQ??m?;?x?'",
+    "?Q??m?;?u?'",
+    "R^??m?;��?'",
+    "?Q??m?;��`'",
+    "? ?}&?#??X\b"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 659.0,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 432.5,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "kn-66a21179-2adc-4b19-a109-880cf4674d7d",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
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+   "n_returned": 10,
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+   "error": null,
+   "clean": false,
+   "false_positives": 10
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "?of?7???",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "mem-f3b37427-b7d1-4f7e-b32c-0241a20ce8da",
+    "art-80ca3d31-84dc-4502-83f4-538372b9764f"
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+   "rank_correct": 8,
+   "rank_stale": null
+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "7?e?7???\f3?",
+    "?of?7???",
+    "?ǚ?7??????",
+    "[?MO5????G",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3"
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+   "rank_stale": null
+  },
+  {
+   "id": "q38",
+   "category": "superseded",
+   "query": "is MCP still the live integration layer",
+   "returned": [
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "%???2??jH??",
+    "???Ͼd??W\b?",
+    "??o?'?B???k",
+    "? ?}&?#??X\b",
+    "63307ac5-cf6b-46e0-8296-07503b461cfa",
+    "? ?}&?#??X\b",
+    "?of?7???"
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+   "outranks": false,
+   "rank_correct": null,
+   "rank_stale": null
+  }
+ ]
+}

tools/retrieval-eval/results-main.json

@@ -0,0 +1,945 @@
+{
+ "label": "main-r1",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-main",
+ "soul_md5": "caf822425540114984bfcd713ad37162",
+ "corpus": "/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json",
+ "corpus_nodes": 78768,
+ "corpus_edges": 14214,
+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7893,
+ "wall_clock_s": 45.9,
+ "child_pid": 78554,
+ "child_confirmed_dead": true,
+ "aggregate": {
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+  "nonsense_clean": "2/3",
+  "superseded_outranks": "1/3",
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+   "paraphrase": {
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+   "id": "q01",
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+   "query": "unjailbreakable",
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+   "id": "q03",
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+  {
+   "id": "q05",
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+   "query": "inferencenodemanager",
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+   "id": "q06",
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+   "query": "clear-eyed",
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+   "id": "q07",
+   "category": "phrase",
+   "query": "patterns not returns",
+   "returned": [
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+    "?ǚ?7??????",
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+   "id": "q08",
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+   "query": "Grandma Lucas",
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+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "ԍ????X????",
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "?ǚ?7??????",
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+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "????7???Ջ3",
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+   "category": "phrase",
+   "query": "Sarah Bishop",
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+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
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+    "? ?}&?#??X\b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "mem-a9a9ce95-0d64-46eb-9db8-ff81d78ade35",
+    "mem-b8ecd23e-77ce-42f7-984c-f51453fec16d"
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+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
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+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
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+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "7?e?7???\f3?",
+    "?of?7???",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
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+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "returned": [
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+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a",
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+    "mem-a3c97012-5fa3-4915-a839-2c75c72005e0",
+    "mem-7cd90611-88a3-423d-a38a-0db2812952fa",
+    "bl-07375bf9-a169-42cd-adb3-7d32b25982f0",
+    "bl-ec84b63d-b278-4944-8d7f-4aa7a51c0315",
+    "7?e?7???\f3?",
+    "?of?7???",
+    "? ?}&?#??X\b"
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+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "????7???Ջ3",
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+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
+    "? ?}&?#??X\b",
+    "kn-a31e1001-342e-4deb-a2e6-6d02d1f22dee",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
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+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "?of?7???",
+    "????7???Ջ3",
+    "kn-d97920d0-1649-4223-9508-c0bb621e7fc0",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "kn-81c24d13-a73b-4767-819c-dafaacc1498e",
+    "? ?}&?#??X\b"
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+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    "7?e?7???\f3?",
+    "? ?}&?#??X\b",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "??o?'?B???k",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "? ?}&?#??X\b",
+    "?of?7???"
+   ],
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+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "7?e?7???\f3?",
+    "?of?7???",
+    "imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "kn-83bb86c6-521d-416c-a86e-6e29c2d8f102",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 9,
+   "latency_ms": 1352.5,
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+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?",
+    "??o?'?B???k",
+    "? ?}&?#??X\b",
+    "kn-0625e393-067c-4bba-8389-7e1b79265142",
+    "ע?RGk?\tH(?"
+   ],
+   "n_returned": 10,
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+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "7?e?7???\f3?",
+    "?of?7???",
+    "art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356"
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+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "??????X??2c",
+    "ԍ????X????",
+    "dR????X?-?S",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "dz????Xƹ?i",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1327.3,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "?of?7???",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "dR????X?-?S",
+    "dz????Xƹ?i",
+    "ԍ????X????",
+    "??????X??2c",
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "????7???Ջ3",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "?ǚ?7??????",
+    "7?e?7???\f3?",
+    "??f?7???",
+    "? ?}&?#??X\b",
+    "%???2??jH??",
+    "kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
+    "? ?}&?#??X\b",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
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+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+    "? ?}&?#??X\b",
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+  {
+   "id": "q29",
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+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
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+   "returned": [
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+   "returned": [
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+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
+    "? ?}&?#??X\b",
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+    "7?e?7???\f3?",
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+ ]
+}

tools/retrieval-eval/results-semseed-r2.json

@@ -0,0 +1,957 @@
+{
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+ "soul_md5": "ab0c82781215f43d4907bd6f39d3615b",
+ "corpus": "/Users/timlingo/neuron-eval-corpora/snapshot-pre-repair-20260806-embedded.json",
+ "corpus_nodes": 78768,
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+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-semseed/tools/retrieval-eval/gold_set.json",
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+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "knw-0087493b-25cd-45b0-bf46-c078c5b49718",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6"
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+   "precision@5": 0.6,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q09",
+   "category": "phrase",
+   "query": "Grandma Lucas",
+   "returned": [
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "? ?}&?#??X\b",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
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+   "precision@5": 0.6,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "ԍ????X????",
+    "project-harmonic-framework",
+    "?ǚ?7??????",
+    "project-harmonic-framework_com",
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "??????X??2c",
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "????7???Ջ3",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356"
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+   "mrr@10": 0.1111111111111111
+  },
+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
+   ],
+   "n_returned": 10,
+   "latency_ms": 532.5,
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+   "mrr@10": 0.1111111111111111
+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "bl-31abf75b-998f-4a4f-a6dd-8204119e0451",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
+    "mem-82b93b21-a865-410f-9ec1-fc54121d9bb5",
+    "bl-6f99e111-7055-4635-9831-a489747ce418",
+    "bl-967536a0-d49d-44fb-8cfb-b31b40bcbfae",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "bl-8b58d9bc-352b-4842-a7f8-a6254b5d1e25",
+    "bl-39cec462-c80c-4970-a3aa-91fe83053bde"
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+   "n_returned": 10,
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+   "recall@5": 0.2857142857142857,
+   "recall@10": 0.2857142857142857,
+   "precision@5": 0.8,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "returned": [
+    "7774a16c-1027-4e3b-a21e-67f1f95a4acd",
+    "8f3abb0d-77ed-4af3-9f4d-ba62cd198886",
+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a",
+    "?",
+    "mem-dba009a2-d2ea-4f5a-b9e8-0f04bc9ab32f",
+    "?",
+    "mem-7cd90611-88a3-423d-a38a-0db2812952fa",
+    "?",
+    "bl-07375bf9-a169-42cd-adb3-7d32b25982f0",
+    "?"
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+   "recall@5": 1.0,
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+   "precision@5": 0.2,
+   "mrr@10": 0.3333333333333333
+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "ctx-4a41"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "? ?}&?#??X\b",
+    "54608b69-78b6-4239-b60f-b8206cfecacc",
+    "? ?}&?#??X\b"
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "knw-8fd9836c-cc39-49df-8d61-babda626cc88",
+    "?of?7???",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "? ?}&?#??X\b",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "????7???Ջ3"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1402.4,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "7?e?7???\f3?",
+    "knw-f6ed7d00-bf7d-42ce-9e40-77cf3406e918",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "??o?'?B???k",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "? ?}&?#??X\b",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "?of?7???",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
+    "ctx-cc7f",
+    "ctx-4a41",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "a1000001-0000-0000-0000-000000000001"
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+   "n_returned": 9,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
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+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "? ?}&?#??X\b",
+    "a708dd6e-fe73-4f2f-a21e-89daa0985487",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1622.4,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "bl-2515d870-e35e-443b-ba20-5150bbc73fed",
+    "? ?}&?#??X\b",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "bl-8848929a-a23a-46bc-a2c7-fe3a3bc1cddf",
+    "? ?}&?#??X\b",
+    "bl-e93858c4-7cac-4b1a-bb62-490790d4c3f3",
+    "? ?}&?#??X\b",
+    "bl-286b562a-5299-40e0-a32a-afa9cbdfe995"
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+   "n_returned": 10,
+   "latency_ms": 1412.0,
+   "error": null,
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+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "?of?7???",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8"
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+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "????7???Ջ3",
+    "a1000001-0000-0000-0000-000000000001",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "?ǚ?7??????",
+    "mem-024598a9-ed2e-4eeb-b1e1-5410856ff132",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "7?e?7???\f3?"
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+   "n_returned": 10,
+   "latency_ms": 1535.9,
+   "error": null,
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+   "recall@5": 0.0,
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
+    "mem-bbb126a1-b297-42bb-86be-796871829c94",
+    "knw-f9ce17a7-17fc-431f-8f23-695b670ec4fa",
+    "mem-45022957-2d78-48aa-a714-16d6eca52e0f",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "a1000001-0000-0000-0000-000000000001"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1565.7,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "?ǚ?7??????",
+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "7?e?7???\f3?",
+    "ctx-bb74",
+    "??S?7???",
+    "knw-f671966c-3387-4848-abca-b5deec122e00"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1279.3,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "? ?}&?#??X\b",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3"
+   ],
+   "n_returned": 10,
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+   "query": "Grandma Lucas stroke February 2006 goodbye window",
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+   "query": "Swarm Architecture containment lateral worker",
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+   "id": "q35",
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+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
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+    "?V?",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
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+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
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+   "id": "q37",
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+}

tools/retrieval-eval/results-semseed.json

@@ -0,0 +1,957 @@
+{
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+   "query": "Grandma Lucas",
+   "returned": [
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "? ?}&?#??X\b",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
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+   "precision@5": 0.6,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "ԍ????X????",
+    "project-harmonic-framework",
+    "?ǚ?7??????",
+    "project-harmonic-framework_com",
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "??????X??2c",
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "????7???Ջ3",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356"
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+   "mrr@10": 0.1111111111111111
+  },
+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
+   ],
+   "n_returned": 10,
+   "latency_ms": 531.4,
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+   "precision@5": 0.0,
+   "mrr@10": 0.1111111111111111
+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "bl-31abf75b-998f-4a4f-a6dd-8204119e0451",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
+    "mem-82b93b21-a865-410f-9ec1-fc54121d9bb5",
+    "bl-6f99e111-7055-4635-9831-a489747ce418",
+    "bl-967536a0-d49d-44fb-8cfb-b31b40bcbfae",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "bl-8b58d9bc-352b-4842-a7f8-a6254b5d1e25",
+    "bl-39cec462-c80c-4970-a3aa-91fe83053bde"
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+   "n_returned": 10,
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+   "recall@5": 0.2857142857142857,
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+   "precision@5": 0.8,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "returned": [
+    "7774a16c-1027-4e3b-a21e-67f1f95a4acd",
+    "8f3abb0d-77ed-4af3-9f4d-ba62cd198886",
+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a",
+    "?",
+    "mem-dba009a2-d2ea-4f5a-b9e8-0f04bc9ab32f",
+    "?",
+    "mem-7cd90611-88a3-423d-a38a-0db2812952fa",
+    "?",
+    "bl-07375bf9-a169-42cd-adb3-7d32b25982f0",
+    "?"
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+   "n_returned": 10,
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+   "recall@5": 1.0,
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+   "mrr@10": 0.3333333333333333
+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "? ?}&?#??X\b",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "ctx-4a41"
+   ],
+   "n_returned": 10,
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-a31e1001-342e-4deb-a2e6-6d02d1f22dee",
+    "54608b69-78b6-4239-b60f-b8206cfecacc",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1"
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+   "mrr@10": 0.5
+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "knw-8fd9836c-cc39-49df-8d61-babda626cc88",
+    "?of?7???",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "? ?}&?#??X\b",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "????7???Ջ3"
+   ],
+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "7?e?7???\f3?",
+    "knw-f6ed7d00-bf7d-42ce-9e40-77cf3406e918",
+    "??o?'?B???k",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "? ?}&?#??X\b",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "? ?}&?#??X\b",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329"
+   ],
+   "n_returned": 10,
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "?of?7???",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
+    "ctx-cc7f",
+    "ctx-4a41",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "a1000001-0000-0000-0000-000000000001"
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+   "n_returned": 9,
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+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
+    "knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
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+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "? ?}&?#??X\b",
+    "a708dd6e-fe73-4f2f-a21e-89daa0985487",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "? ?}&?#??X\b"
+   ],
+   "n_returned": 10,
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+   "error": null,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "bl-2515d870-e35e-443b-ba20-5150bbc73fed",
+    "? ?}&?#??X\b",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "bl-8848929a-a23a-46bc-a2c7-fe3a3bc1cddf",
+    "? ?}&?#??X\b",
+    "bl-e93858c4-7cac-4b1a-bb62-490790d4c3f3",
+    "? ?}&?#??X\b",
+    "bl-286b562a-5299-40e0-a32a-afa9cbdfe995"
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+   "n_returned": 10,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
+    "7?e?7???\f3?",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+    "knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "kn-f8974b26-78a6-4aad-b893-19a73b20013d",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "?of?7???",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1710.4,
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+   "precision@5": 0.2,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "????7???Ջ3",
+    "a1000001-0000-0000-0000-000000000001",
+    "8cbb60c5-4999-4ec1-8682-2592aedc4249",
+    "?ǚ?7??????",
+    "mem-024598a9-ed2e-4eeb-b1e1-5410856ff132",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "7?e?7???\f3?"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1565.1,
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+   "recall@5": 0.0,
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
+    "mem-bbb126a1-b297-42bb-86be-796871829c94",
+    "knw-f9ce17a7-17fc-431f-8f23-695b670ec4fa",
+    "mem-45022957-2d78-48aa-a714-16d6eca52e0f",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "a1000001-0000-0000-0000-000000000001"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1629.0,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
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+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "?ǚ?7??????",
+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "7?e?7???\f3?",
+    "ctx-bb74",
+    "??S?7???",
+    "knw-f671966c-3387-4848-abca-b5deec122e00"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1326.5,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "? ?}&?#??X\b",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "? ?}&?#??X\b",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "art-ee615cdb-e599-423d-9a4d-977859390ed3"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1382.6,
+   "error": null,
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+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.2
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "? ?}&?#??X\b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "? ?}&?#??X\b",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "? ?}&?#??X\b",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
+   ],
+   "n_returned": 10,
+   "latency_ms": 1530.5,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.18181818181818182,
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+    "54608b69-78b6-4239-b60f-b8206cfecacc",
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+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
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+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "? ?}&?#??X\b",
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+    "? ?}&?#??X\b",
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+   "mrr@10": 0.25
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
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+   "query": "hope won inside the narrative preface",
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+  {
+   "id": "q32",
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+   "query": "man of the house six years old expectation",
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+    "? ?}&?#??X\b",
+    "4f698ae6-c40e-464e-9798-50350991a188",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
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+  {
+   "id": "q33",
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+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 756.0,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 517.1,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [
+    "art-4a99aa1a-489b-4b43-958b-25217adb1aad",
+    "?V?",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "?m?\\}Q??6??",
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+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
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+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "7?e?7???\f3?",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "? ?}&?#??X\b",
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+    "?of?7???",
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+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "? ?}&?#??X\b",
+    "12082f7e-e320-438b-bd65-083d8259748f",
+    "6de314bf-5c4c-4cfc-871f-fa2e422d45e6",
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+  {
+   "id": "q38",
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+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
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+    "%???2??jH??"
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+ ]
+}

tools/retrieval-eval/results-wordstart-r2.json

@@ -0,0 +1,948 @@
+{
+ "label": "wordstart-r2",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-wordstart",
+ "soul_md5": "32d4cf77672658a5f49dc7c9213e3ba2",
+ "corpus": "/Users/timlingo/neuron-eval-corpora/snapshot-pre-repair-20260806-embedded.json",
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+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
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+ "rows": [
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+   "query": "unjailbreakable",
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+  },
+  {
+   "id": "q07",
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+    "mem-a4a9dfc3-e40b-49b3-b1e1-060e8be2f482",
+    "project-Imprint__system_design__ADRs__tech_strategy__integration_patterns__governance_",
+    "project-Imprint__analysis_patterns__data_storytelling__SQL__dashboards__insight_framing_",
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+   "query": "Grandma Lucas",
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+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "project-harmonic-framework",
+    "bl-798d135f-3987-4ccd-8de6-70ca2f358337",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "project-harmonic-framework_com",
+    "bl-680b24a9-edc3-4a9d-847a-bff0b46b568c",
+    "tag-harmonic-design",
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+    "tag-harmonic-framework",
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+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
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+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
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+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "tag-sarah",
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+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
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+    "bl-31abf75b-998f-4a4f-a6dd-8204119e0451",
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+    "bl-8b58d9bc-352b-4842-a7f8-a6254b5d1e25",
+    "?Q??m?;?u?'",
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+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
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+    "8f3abb0d-77ed-4af3-9f4d-ba62cd198886",
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+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
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+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
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+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
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+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
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+    "bl-798d135f-3987-4ccd-8de6-70ca2f358337",
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+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
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+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
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+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
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+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
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+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
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+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
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+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
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+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
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+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
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+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
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+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
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+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
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+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
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+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
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+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "tag-childhood",
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+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
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+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
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+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
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+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
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+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "tag-trailer-park-paladins",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "project-trailer-park-paladins",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
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+   "mrr@10": 0.5
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
+    "bl-0fac287f-f4c0-4f15-bc4d-ff7f8a7af3ae",
+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
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+  {
+   "id": "q31",
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+   "query": "hope won inside the narrative preface",
+   "returned": [
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+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
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+    "tag-hope",
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+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "knw-528dbc37-eabc-4b75-a7a5-65bf38d6018a",
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+    "kn-6061318f-046b-4935-907d-8eafdce14930"
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+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 350.7,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 254.6,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 345.8,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "mem-f3b37427-b7d1-4f7e-b32c-0241a20ce8da",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "tag-__darma____cgi____patents____self-improvement____character-preservation____autonomous____architecture__",
+    "kn-b7e98d63-8b83-4911-b4d0-990602a7f575",
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+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "mem-6f0b2b45-90c1-4356-ac01-3daac05b09c8",
+    "12082f7e-e320-438b-bd65-083d8259748f",
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+    "13705072-4515-4124-963d-083af490494f",
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+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "de3b6428-b76c-4c44-90e0-bf1dd6998027"
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+  },
+  {
+   "id": "q38",
+   "category": "superseded",
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+   "returned": [
+    "5fcba804-eb5b-48ec-82da-146b1c6bb50d",
+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
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+    "bl-c5c6571e-118f-47c7-8cbb-3ed0ebf64a51",
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+ ]
+}

tools/retrieval-eval/results-wordstart.json

@@ -0,0 +1,948 @@
+{
+ "label": "wordstart",
+ "soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-wordstart",
+ "soul_md5": "32d4cf77672658a5f49dc7c9213e3ba2",
+ "corpus": "/Users/timlingo/neuron-eval-corpora/snapshot-pre-repair-20260806-embedded.json",
+ "corpus_nodes": 78768,
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+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7894,
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+ "rows": [
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+   "query": "unjailbreakable",
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+  {
+   "id": "q02",
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+    "bl-b28d7256-6f74-4567-bd90-40d0ef2a6d78",
+    "project-engram",
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+    "project-engram-lang",
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+   "query": "cartabandonedevent",
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+    "bl-c1765767-3e27-449a-8c94-10411d1eb7c0",
+    "project-Add_inference_url_config_to_Neuron_MCP__Route_summarization_gen_tasks_to_Pantheon__keep_frontier_for_complex_reasoning_"
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+  },
+  {
+   "id": "q07",
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+   "query": "patterns not returns",
+   "returned": [
+    "tag-patterns",
+    "mem-a4a9dfc3-e40b-49b3-b1e1-060e8be2f482",
+    "project-Imprint__system_design__ADRs__tech_strategy__integration_patterns__governance_",
+    "project-Imprint__analysis_patterns__data_storytelling__SQL__dashboards__insight_framing_",
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+  {
+   "id": "q09",
+   "category": "phrase",
+   "query": "Grandma Lucas",
+   "returned": [
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4"
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+   "precision@5": 0.6,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q10",
+   "category": "phrase",
+   "query": "Directed Harmonic",
+   "returned": [
+    "bl-dcee1887-34c4-4ffa-9119-1e291685ba08",
+    "project-harmonic-framework",
+    "bl-798d135f-3987-4ccd-8de6-70ca2f358337",
+    "mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf",
+    "project-harmonic-framework_com",
+    "bl-680b24a9-edc3-4a9d-847a-bff0b46b568c",
+    "tag-harmonic-design",
+    "bl-92acd4eb-0452-4e8e-9f54-f8cd35170d76",
+    "tag-harmonic-framework",
+    "bl-18a9d1e4-1484-474c-bf6b-c6173212181b"
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+   "precision@5": 0.2,
+   "mrr@10": 0.25
+  },
+  {
+   "id": "q11",
+   "category": "phrase",
+   "query": "Sarah Bishop",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "tag-sarah",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "mem-1f32f73a-952c-41bc-96dc-8b8b70d8a7c1",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "mem-a6cb3b8d-d89c-46fc-931d-e90c560783b0",
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
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+   "precision@5": 0.4,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q12",
+   "category": "phrase",
+   "query": "Directed Autonomous Runtime Modification",
+   "returned": [
+    "mem-e6327f52-2bda-4ce7-9471-2fffd1e172de",
+    "bl-31abf75b-998f-4a4f-a6dd-8204119e0451",
+    "mem-82b93b21-a865-410f-9ec1-fc54121d9bb5",
+    "bl-6f99e111-7055-4635-9831-a489747ce418",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "bl-967536a0-d49d-44fb-8cfb-b31b40bcbfae",
+    "bl-8b58d9bc-352b-4842-a7f8-a6254b5d1e25",
+    "?Q??m?;?u?'",
+    "bl-39cec462-c80c-4970-a3aa-91fe83053bde"
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+   "precision@5": 0.6,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q13",
+   "category": "phrase",
+   "query": "zero-knowledge encrypted backup",
+   "returned": [
+    "deda48cd-5e1a-46cb-bd43-8016afdb3a8a",
+    "8f3abb0d-77ed-4af3-9f4d-ba62cd198886",
+    "7774a16c-1027-4e3b-a21e-67f1f95a4acd",
+    "?",
+    "bl-ec84b63d-b278-4944-8d7f-4aa7a51c0315",
+    "?",
+    "mem-fb44a2fc-7405-41ff-87b3-84643ac07313",
+    "?",
+    "mem-a3c97012-5fa3-4915-a839-2c75c72005e0",
+    "?"
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+   "precision@5": 0.2,
+   "mrr@10": 1.0
+  },
+  {
+   "id": "q14",
+   "category": "paraphrase",
+   "query": "the elderly relative who passed while he stayed away",
+   "returned": [
+    "cb070131-dfd4-4a38-91d7-22b1bde164d2",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "knw-d788a210-613b-4c49-9486-88bbc9d4716f",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "mem-a535f205-bc4c-4058-9171-6263c496044a",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "mem-0228da71-d7f7-4f3b-b7b3-c5eede42b62a",
+    "ctx-4a41"
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+   "mrr@10": 0.0
+  },
+  {
+   "id": "q15",
+   "category": "paraphrase",
+   "query": "a soldier sidelined by illness who refused to quit",
+   "returned": [
+    "b1183213-d659-4759-85d7-5b1f22427fe2",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "mem-16efddd1-c43d-4a42-9d78-f54fb82bd277",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "7452eb8f-be01-4b55-aec1-ff0c29e790f6",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "532277bf-2959-4beb-ae0d-b018c97678ee",
+    "54608b69-78b6-4239-b60f-b8206cfecacc",
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+  },
+  {
+   "id": "q16",
+   "category": "paraphrase",
+   "query": "choosing an uncomfortable fact over a pleasant fiction",
+   "returned": [
+    "tag-fiction",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "mem-8d690e9d-a7e9-4062-b2f8-e2064294e463",
+    "knw-8fd9836c-cc39-49df-8d61-babda626cc88",
+    "mem-ce793303-c5a5-4586-a232-a3426edd9ec7",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "mem-443bd012-fc9a-4088-b236-de5157a1ef92",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "mem-ca4d6a34-d354-413f-bc86-126cc17ca81c"
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+  },
+  {
+   "id": "q17",
+   "category": "paraphrase",
+   "query": "a tight payload beats a bloated one",
+   "returned": [
+    "bl-680b24a9-edc3-4a9d-847a-bff0b46b568c",
+    "bl-798d135f-3987-4ccd-8de6-70ca2f358337",
+    "08f0d1e2-8d0e-42e3-9f0a-8186ae31ec7e",
+    "knw-08559f5c-2306-4220-a146-398c74f1643c",
+    "4da5dbaf-46e5-4f3e-b474-f60d9f8241d3",
+    "knw-f6ed7d00-bf7d-42ce-9e40-77cf3406e918",
+    "mem-434be7c8-88cb-4039-b79a-1da4ac4de783",
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+    "bl-79ce4464-5dd6-49bd-9b0c-9803549d0665"
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+  },
+  {
+   "id": "q18",
+   "category": "paraphrase",
+   "query": "if you are able and nobody is coming the job is yours",
+   "returned": [
+    "bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "mem-e5cc63c0-8701-49d6-855a-e387fe087771",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "mem-75e490d1-f0a9-4b73-8cfc-8daecfaf6f38",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "a1000001-0000-0000-0000-000000000010",
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+    "bfad516b-c306-4c4c-874a-a347c46c05c2",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc"
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+  },
+  {
+   "id": "q19",
+   "category": "paraphrase",
+   "query": "learning is the wealth creditors cannot seize",
+   "returned": [
+    "tag-learning",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
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+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
+    "a1000001-0000-0000-0000-000000000010",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
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+  },
+  {
+   "id": "q20",
+   "category": "paraphrase",
+   "query": "reliability proven by track record not assertion",
+   "returned": [
+    "mem-cde58b77-50d3-4bac-9581-e70a4c02c015",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
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+    "mem-8d699e2c-ac2a-4742-bb62-b6da00f4b10e",
+    "knw-f671966c-3387-4848-abca-b5deec122e00",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "mem-53d6adf0-cd08-4707-a237-daa5e65c7298",
+    "a708dd6e-fe73-4f2f-a21e-89daa0985487",
+    "knw-6b48dce2-f21c-452a-9db5-4e6aa61c87ca",
+    "bl-ef2bac68-e119-4139-b529-c7a1404ae3ac"
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+  {
+   "id": "q21",
+   "category": "paraphrase",
+   "query": "boundaries that enable instead of confine",
+   "returned": [
+    "bl-8dd70cac-866d-4ff2-b9fe-b4b3c5f094bb",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "bl-2515d870-e35e-443b-ba20-5150bbc73fed",
+    "bl-0e8f4880-7b24-43aa-aed9-ad4d9fc73ff8",
+    "project-Source_kn-6f248a50__Add_containment_rules__convergence__location-independence__failure_modes_",
+    "bl-8848929a-a23a-46bc-a2c7-fe3a3bc1cddf",
+    "bl-205141ad-b2a0-4d93-86d0-89eb0723e1bd",
+    "bl-e93858c4-7cac-4b1a-bb62-490790d4c3f3",
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+  },
+  {
+   "id": "q22",
+   "category": "paraphrase",
+   "query": "what shifts tells you where to cut a system apart",
+   "returned": [
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+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
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+    "bl-2b00aeb0-c0fa-4a9f-8f30-4207e98b3d52",
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+    "34356a36-0df5-4020-8dcc-5e7a423f8d4c",
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+  },
+  {
+   "id": "q23",
+   "category": "paraphrase",
+   "query": "a mind that compounds instead of resetting each day",
+   "returned": [
+    "bl-8dd70cac-866d-4ff2-b9fe-b4b3c5f094bb",
+    "mem-b43f6ef4-2f5a-418d-b5ce-3f21520cf6b8",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-ed33e669-0790-44cb-a036-958d605c6fea",
+    "a1000001-0000-0000-0000-000000000001",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "bl-1b58b05c-9305-4f06-a586-a08c96008027",
+    "mem-024598a9-ed2e-4eeb-b1e1-5410856ff132",
+    "ctx-4a41",
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+  },
+  {
+   "id": "q24",
+   "category": "paraphrase",
+   "query": "loved for the unedited self and not the polished exterior",
+   "returned": [
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+    "knw-f9ce17a7-17fc-431f-8f23-695b670ec4fa",
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+    "bl-87c93185-b2bf-40af-ae23-3c830c007abf",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "fce2792a-53fc-4d4a-be3b-42bd6ceb1ba7",
+    "a1000001-0000-0000-0000-000000000001"
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+  },
+  {
+   "id": "q25",
+   "category": "paraphrase",
+   "query": "cheerfulness you arrive at instead of assuming",
+   "returned": [
+    "mem-82158b02-a180-435d-84f0-0b7ce37511b4",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "e4f27651-52c5-43fd-aff3-61d31685b3cd",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "mem-5624ec9d-62ba-4aba-8a3d-6afec6c09dd4",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "mem-a16deccb-16a7-419c-a013-ff824a4daa15",
+    "a1000001-0000-0000-0000-000000000009",
+    "mem-833dbbcd-2400-4594-bb35-93b023049ac0",
+    "kn-13f60407-7b70-4db1-964f-ea1f8196efbd"
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+  },
+  {
+   "id": "q26",
+   "category": "paraphrase",
+   "query": "a childhood offering no solid foundation to inherit",
+   "returned": [
+    "mem-b99efff0-00e6-40c8-9c5b-730330eef33b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
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+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "knw-23c27d3b-e0d2-43a8-a80c-0a44477ae18a",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
+    "tag-childhood",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21"
+   ],
+   "n_returned": 10,
+   "latency_ms": 603.4,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.2
+  },
+  {
+   "id": "q27",
+   "category": "associative",
+   "query": "Grandma Lucas stroke February 2006 goodbye window",
+   "returned": [
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "efe53612-6914-4936-8e3b-1e694eb174e5",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
+   ],
+   "n_returned": 10,
+   "latency_ms": 656.2,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.18181818181818182,
+   "recall@10": 0.45454545454545453,
+   "precision@5": 0.4,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q28",
+   "category": "associative",
+   "query": "Marines hernia sepsis medical ward",
+   "returned": [
+    "bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
+    "54608b69-78b6-4239-b60f-b8206cfecacc",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "mem-9110798f-d0cb-4446-bc2a-14f09b6a09e2",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "art-79042b8b-6192-440f-90b0-60708f7e6325",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71"
+   ],
+   "n_returned": 10,
+   "latency_ms": 536.9,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.07692307692307693,
+   "recall@10": 0.3076923076923077,
+   "precision@5": 0.2,
+   "mrr@10": 0.25
+  },
+  {
+   "id": "q29",
+   "category": "associative",
+   "query": "Sarah Bishop Dyer trailer performance",
+   "returned": [
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "766de879-f9d0-4a07-b6df-b43ee13763d8",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "tag-trailer-park-paladins",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "project-trailer-park-paladins",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
+   ],
+   "n_returned": 10,
+   "latency_ms": 562.4,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.18181818181818182,
+   "recall@10": 0.45454545454545453,
+   "precision@5": 0.4,
+   "mrr@10": 0.5
+  },
+  {
+   "id": "q30",
+   "category": "associative",
+   "query": "Swarm Architecture containment lateral worker",
+   "returned": [
+    "bl-0fac287f-f4c0-4f15-bc4d-ff7f8a7af3ae",
+    "bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
+    "bl-2515d870-e35e-443b-ba20-5150bbc73fed",
+    "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
+    "kn-b36902cc-0b05-44ba-9aa7-800e5dea9ca9",
+    "bl-bea7473c-c687-414c-9c0b-00c509a616c1",
+    "bl-fc6fcb0b-9e4b-40bf-8e88-dbfe4e27c31a",
+    "kn-6f248a50-355b-47bb-aec8-e0e646a9b077",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "mem-ab34c2f7-3243-424b-affa-25555f6cf9cc"
+   ],
+   "n_returned": 10,
+   "latency_ms": 556.6,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q31",
+   "category": "associative",
+   "query": "hope won inside the narrative preface",
+   "returned": [
+    "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
+    "bl-2b00aeb0-c0fa-4a9f-8f30-4207e98b3d52",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
+    "knw-723551f5-1950-42a3-8b89-b6a06913cef0",
+    "tag-hope",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
+   ],
+   "n_returned": 10,
+   "latency_ms": 542.6,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 0.09090909090909091,
+   "recall@10": 0.18181818181818182,
+   "precision@5": 0.2,
+   "mrr@10": 0.25
+  },
+  {
+   "id": "q32",
+   "category": "associative",
+   "query": "man of the house six years old expectation",
+   "returned": [
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "knw-528dbc37-eabc-4b75-a7a5-65bf38d6018a",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "knw-473f3f24-20f6-4f39-8589-3709538eb6ac",
+    "mem-a0b7cfda-bc9e-4f40-b9a9-1722cf3f8263",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-35940684-abc4-42f0-b942-818f66b1f69a",
+    "4f698ae6-c40e-464e-9798-50350991a188",
+    "719aa819-00a9-4f4b-a857-4f9fe5ad44d7",
+    "kn-6061318f-046b-4935-907d-8eafdce14930"
+   ],
+   "n_returned": 10,
+   "latency_ms": 683.5,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0
+  },
+  {
+   "id": "q33",
+   "category": "nonsense",
+   "query": "zqxjvw plimforth grebulon",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 350.4,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q34",
+   "category": "nonsense",
+   "query": "flarnbistle quommetry",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 258.4,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q35",
+   "category": "nonsense",
+   "query": "xxqzzt vurblenacht throom",
+   "returned": [],
+   "n_returned": 0,
+   "latency_ms": 348.4,
+   "error": null,
+   "clean": true,
+   "false_positives": 0
+  },
+  {
+   "id": "q36",
+   "category": "superseded",
+   "query": "is the self-improvement architecture called DARMA or DHARMA",
+   "returned": [
+    "mem-f3b37427-b7d1-4f7e-b32c-0241a20ce8da",
+    "mem-80d7416b-20e9-48a0-b176-b215527e2f56",
+    "tag-__darma____cgi____patents____self-improvement____character-preservation____autonomous____architecture__",
+    "kn-b7e98d63-8b83-4911-b4d0-990602a7f575",
+    "tag-__darma____cgi____patents____self-improvement____character-preservation____autonomous____kotlin____architecture__",
+    "knw-e047bb42-dc5b-4383-9e88-e508dc03abe3",
+    "mem-c17aefb1-38b5-4ced-af50-fe524127e1a4",
+    "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
+    "mem-82b93b21-a865-410f-9ec1-fc54121d9bb5"
+   ],
+   "n_returned": 10,
+   "latency_ms": 664.5,
+   "error": null,
+   "hit@5": 1.0,
+   "recall@5": 1.0,
+   "recall@10": 1.0,
+   "precision@5": 0.2,
+   "mrr@10": 0.5,
+   "outranks": true,
+   "rank_correct": 2,
+   "rank_stale": 8
+  },
+  {
+   "id": "q37",
+   "category": "superseded",
+   "query": "how many provisional patents does Will actually have",
+   "returned": [
+    "mem-6f0b2b45-90c1-4356-ac01-3daac05b09c8",
+    "12082f7e-e320-438b-bd65-083d8259748f",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "13705072-4515-4124-963d-083af490494f",
+    "527ecb25-2587-47eb-8269-73be2431abd4",
+    "6de314bf-5c4c-4cfc-871f-fa2e422d45e6",
+    "a1000001-0000-0000-0000-000000000002",
+    "3cf706a1-3825-45d8-b0a9-06cae6cdf5b8",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "de3b6428-b76c-4c44-90e0-bf1dd6998027"
+   ],
+   "n_returned": 10,
+   "latency_ms": 747.3,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 1.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.125,
+   "outranks": true,
+   "rank_correct": 8,
+   "rank_stale": null
+  },
+  {
+   "id": "q38",
+   "category": "superseded",
+   "query": "is MCP still the live integration layer",
+   "returned": [
+    "5fcba804-eb5b-48ec-82da-146b1c6bb50d",
+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
+    "bl-c8c19362-430b-4817-9cf4-9e85e0099c64",
+    "bl-c5c6571e-118f-47c7-8cbb-3ed0ebf64a51",
+    "mem-101e81b4-8097-4749-8d8d-7bb66de34517",
+    "ctx-3a55",
+    "86228228-7adf-41fb-b4c4-9ceea87953ae",
+    "4509ed62-9fb2-48b8-9038-ac569fca9604",
+    "bl-4f7b651b-6b33-449c-8a3b-cfce12ce984b",
+    "mem-3a2cf162-d93b-4f29-86f2-5066fb7fe1f5"
+   ],
+   "n_returned": 10,
+   "latency_ms": 504.2,
+   "error": null,
+   "hit@5": 0.0,
+   "recall@5": 0.0,
+   "recall@10": 0.0,
+   "precision@5": 0.0,
+   "mrr@10": 0.0,
+   "outranks": false,
+   "rank_correct": null,
+   "rank_stale": 5
+  }
+ ]
+}

tools/retrieval-eval/run_comparison.sh

@@ -0,0 +1,98 @@
+#!/usr/bin/env bash
+# run_comparison.sh — the whole harness, end to end, from two git refs.
+#
+# Builds a soul from each ref, boots each on its own throwaway port with its own
+# throwaway HOME and its own disposable copy of the corpus, runs the gold set N
+# times per ref, and prints the comparison with its noise threshold.
+#
+# SAFETY: never touches ~/.neuron, /Applications/Neuron*, ~/neuron-dev-stack, or
+# any running service. Sources are exported with `git archive` into a scratch
+# dir, so no worktree or branch state is mutated either. Ports are checked
+# against the live set before anything boots. Every soul this script starts is
+# killed and confirmed dead by run_eval.py; the sweep at the end is a backstop.
+#
+# usage:
+#   run_comparison.sh [--baseline main] [--candidate feat/recall-through-activation]
+#                     [--repeats 3] [--corpus <snapshot.json>] [--repo <path>]
+set -euo pipefail
+
+BASELINE="main"
+CANDIDATE="feat/recall-through-activation"
+REPEATS=3
+CORPUS="$HOME/neuron-memory-backups/snapshot-pre-repair-20260806.json"
+REPO="$HOME/Development/neuron"
+BASE_PORT=7893
+
+while [ $# -gt 0 ]; do
+  case "$1" in
+    --baseline)  BASELINE="$2"; shift 2 ;;
+    --candidate) CANDIDATE="$2"; shift 2 ;;
+    --repeats)   REPEATS="$2"; shift 2 ;;
+    --corpus)    CORPUS="$2"; shift 2 ;;
+    --repo)      REPO="$2"; shift 2 ;;
+    *) echo "unknown arg: $1" >&2; exit 2 ;;
+  esac
+done
+
+HERE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+WORK="$(mktemp -d "${TMPDIR:-/tmp}/retrieval-eval.XXXXXX")"
+trap 'rm -rf "$WORK"' EXIT
+
+[ -f "$CORPUS" ] || { echo "no corpus at $CORPUS" >&2; exit 2; }
+echo "corpus: $CORPUS ($(du -h "$CORPUS" | cut -f1))"
+
+slug() { printf '%s' "$1" | tr '/' '-'; }
+
+build_ref() {   # ref -> binary path
+  local ref="$1" out="$WORK/soul-$(slug "$1")"
+  local src="$WORK/src-$(slug "$1")"
+  mkdir -p "$src"
+  git -C "$REPO" archive "$ref" | tar -x -C "$src"
+  "$HERE/build-soul.sh" "$src" "$out" >&2
+  printf '%s' "$out"
+}
+
+echo "== building $BASELINE =="
+BIN_A="$(build_ref "$BASELINE")"
+echo "== building $CANDIDATE =="
+BIN_B="$(build_ref "$CANDIDATE")"
+
+echo "== validating the gold set against this corpus =="
+python3 "$HERE/build_gold_set.py" "$CORPUS" --check
+
+port=$BASE_PORT
+run_one() { # binary label out
+  echo "== $2 =="
+  python3 "$HERE/run_eval.py" --soul "$1" --corpus "$CORPUS" --label "$2" \
+      --port "$port" --out "$3"
+  port=$((port + 1))
+}
+
+A_MAIN="$WORK/results-a-1.json"; B_MAIN="$WORK/results-b-1.json"
+A_REP=(); B_REP=()
+for i in $(seq 1 "$REPEATS"); do
+  a="$WORK/results-a-$i.json"; b="$WORK/results-b-$i.json"
+  run_one "$BIN_A" "$(slug "$BASELINE")-r$i" "$a"
+  run_one "$BIN_B" "$(slug "$CANDIDATE")-r$i" "$b"
+  [ "$i" -gt 1 ] && { A_REP+=("$a"); B_REP+=("$b"); }
+done
+
+cp "$A_MAIN" "$HERE/results-$(slug "$BASELINE").json"
+cp "$B_MAIN" "$HERE/results-$(slug "$CANDIDATE").json"
+
+echo
+python3 "$HERE/compare.py" \
+  --baseline "$A_MAIN" --candidate "$B_MAIN" \
+  ${A_REP[@]+--repeats-baseline "${A_REP[@]}"} \
+  ${B_REP[@]+--repeats-candidate "${B_REP[@]}"} \
+  --out "$HERE/comparison-$(slug "$BASELINE")-vs-$(slug "$CANDIDATE").json"
+
+# Backstop: run_eval.py kills and confirms its own child, but a crashed run
+# could leak one. Leaving a soul running is how the live engine got squeezed.
+STRAY=$(pgrep -f "$WORK/soul-" || true)
+if [ -n "$STRAY" ]; then
+  echo "!! stray eval souls, killing: $STRAY" >&2
+  kill -9 $STRAY 2>/dev/null || true
+fi
+pgrep -f "$WORK/soul-" >/dev/null && { echo "!! STILL RUNNING" >&2; exit 5; }
+echo "process check: no eval souls running"

tools/retrieval-eval/run_eval.py

@@ -0,0 +1,398 @@
+#!/usr/bin/env python3
+"""
+run_eval.py — measure one soul build's retrieval against the gold set.
+
+WHAT IT MEASURES, AND WHY IT BOOTS A REAL SOUL
+    The point is Will's designed retrieval — spreading activation over the
+    weighted directed graph with four-factor multiplicative scoring — not a
+    Python re-implementation of it. A re-implementation would measure my
+    reading of the design; booting the compiled binary measures the design. So
+    this harness compiles the actual `soul.el` amalgam (build-soul.sh) and asks
+    it over HTTP, exactly as the MCP wrapper and the app do.
+
+SAFETY — read this before changing anything here
+    * Boots on a THROWAWAY port with a THROWAWAY $HOME and a THROWAWAY COPY of
+      the corpus. Refuses to use 7770 / 8742 / 7779 / 17779 / 7771.
+    * ENGRAM_URL / SOUL_ENGRAM_URL are UNSET and SOUL_ISE_URL is pinned to a
+      dead port. This is not belt-and-braces: the periodic engram sync resolves
+      its source as env(SOUL_ISE_URL) -> state -> DEFAULT http://localhost:8742,
+      so leaving it unset makes an "isolated" run silently pull the operator's
+      LIVE brain. (Learned the hard way on 2026-08-03; see the same note in
+      scripts/verify-soul-contract.sh.)
+    * Every process this file starts is tracked and killed in a finally block,
+      then CONFIRMED dead by pid probe, and the confirmation is written into the
+      results file. A run that cannot confirm its child is dead exits non-zero.
+    * Activation is a STATEFUL read by design (patent claim 29: traversal
+      updates last-activation and increments activation counts). The corpus copy
+      is therefore per-run and disposable, and every run starts from a byte-
+      identical copy so two configurations see the same starting graph.
+
+usage:
+  python3 run_eval.py --soul <binary> --corpus <snapshot.json> --label main \
+      [--port 7893] [--gold gold_set.json] [--limit 10] [--out results-main.json]
+"""
+import argparse
+import json
+import os
+import shutil
+import signal
+import subprocess
+import sys
+import tempfile
+import time
+import urllib.error
+import urllib.parse
+import urllib.request
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+FORBIDDEN_PORTS = {7770, 8742, 7779, 17779, 7771, 8080}
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# metrics
+# ─────────────────────────────────────────────────────────────────────────────
+def recall_at_k(returned, relevant, k):
+    if not relevant:
+        return None
+    return len(set(returned[:k]) & set(relevant)) / len(relevant)
+
+
+def hit_at_k(returned, relevant, k):
+    if not relevant:
+        return None
+    return 1.0 if set(returned[:k]) & set(relevant) else 0.0
+
+
+def precision_at_k(returned, relevant, k):
+    """Fixed denominator k, as in docs/research/graphrag_eval/score.py.
+
+    Fixed denominator penalises an empty result and a page of junk equally,
+    which is what we want: a retriever that returns nothing is not 'precise'.
+    """
+    if not relevant:
+        return None
+    return len(set(returned[:k]) & set(relevant)) / k
+
+
+def mrr(returned, relevant, k):
+    if not relevant:
+        return None
+    rel = set(relevant)
+    for i, nid in enumerate(returned[:k], start=1):
+        if nid in rel:
+            return 1.0 / i
+    return 0.0
+
+
+def mean(vals):
+    vals = [v for v in vals if v is not None]
+    return sum(vals) / len(vals) if vals else 0.0
+
+
+def pct(vals):
+    return f"{100 * mean(vals):.1f}%"
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# soul lifecycle
+# ─────────────────────────────────────────────────────────────────────────────
+class Soul:
+    def __init__(self, binary, corpus, port, verbose=True):
+        if port in FORBIDDEN_PORTS:
+            raise SystemExit(f"REFUSING: port {port} is a live service port.")
+        self.binary = os.path.abspath(binary)
+        self.corpus = os.path.abspath(corpus)
+        self.port = port
+        self.verbose = verbose
+        self.home = None
+        self.proc = None
+        self.pid = None
+        self.log = None
+        self.confirmed_dead = None
+
+    @property
+    def base(self):
+        return f"http://127.0.0.1:{self.port}"
+
+    def start(self, boot_timeout=180):
+        self.home = tempfile.mkdtemp(prefix="retrieval-eval-home.")
+        snap = os.path.join(self.home, "corpus.json")
+        t0 = time.time()
+        shutil.copyfile(self.corpus, snap)   # per-run disposable copy, never the source
+        self.log = os.path.join(self.home, "soul.log")
+
+        env = {k: v for k, v in os.environ.items()
+               if k not in ("ENGRAM_URL", "ENGRAM_API_KEY", "SOUL_ENGRAM_URL",
+                            "ANTHROPIC_API_KEY", "NEURON_LLM_API_KEY", "SOUL_IDENTITY",
+                            "SOUL_API_KEY")}
+        env.update({
+            "HOME": self.home,
+            "NEURON_PORT": str(self.port),
+            "SOUL_CGI_ID": f"ntn-retrieval-eval-{os.getpid()}",
+            "SOUL_ENGRAM_PATH": snap,
+            "NEURON_API_URL": "http://127.0.0.1:9",   # dead port
+            "SOUL_ISE_URL": "http://127.0.0.1:9",     # dead port — see SAFETY above
+            # Park the background loops for an hour so heartbeat/consolidation
+            # cannot mutate the graph between queries and make runs unrepeatable.
+            "SOUL_TICK_MS": "3600000",
+            "SOUL_HEARTBEAT_MS": "3600000",
+            "SOUL_REFRESH_MS": "3600000",
+        })
+        with open(self.log, "wb") as lf:
+            self.proc = subprocess.Popen([self.binary], env=env, stdout=lf, stderr=lf,
+                                         start_new_session=True)
+        self.pid = self.proc.pid
+        if self.verbose:
+            print(f"  booted pid={self.pid} port={self.port} home={self.home}")
+
+        deadline = time.time() + boot_timeout
+        while time.time() < deadline:
+            if self.proc.poll() is not None:
+                raise RuntimeError(f"soul exited during boot: {self._log_tail()}")
+            rss = self._rss_kb()
+            if rss and rss > 6 * 1024 * 1024:
+                self.stop()
+                raise RuntimeError(f"soul RSS {rss}KB > 6GB — aborted")
+            try:
+                with urllib.request.urlopen(f"{self.base}/health", timeout=2) as r:
+                    if r.status == 200:
+                        if self.verbose:
+                            print(f"  healthy in {time.time() - t0:.1f}s, RSS={self._rss_kb()}KB")
+                        return
+            except Exception:
+                pass
+            time.sleep(0.5)
+        self.stop()
+        raise RuntimeError(f"soul never healthy on {self.base}: {self._log_tail()}")
+
+    def _rss_kb(self):
+        try:
+            out = subprocess.run(["ps", "-o", "rss=", "-p", str(self.pid)],
+                                 capture_output=True, text=True, timeout=5).stdout.strip()
+            return int(out) if out else None
+        except Exception:
+            return None
+
+    def _log_tail(self, n=15):
+        try:
+            with open(self.log, encoding="utf-8", errors="replace") as fh:
+                return "\n".join(fh.read().splitlines()[-n:])
+        except Exception:
+            return "(no log)"
+
+    def recall(self, query, limit, timeout=60):
+        url = f"{self.base}/api/neuron/recall?query={urllib.parse.quote(query)}&limit={limit}"
+        t0 = time.perf_counter()
+        try:
+            with urllib.request.urlopen(url, timeout=timeout) as r:
+                raw = r.read().decode("utf-8", "replace")
+            ms = (time.perf_counter() - t0) * 1000
+        except Exception as exc:
+            return [], (time.perf_counter() - t0) * 1000, f"{type(exc).__name__}: {exc}"
+        try:
+            arr = json.loads(raw)
+        except Exception:
+            return [], ms, f"unparseable response ({len(raw)}B)"
+        if not isinstance(arr, list):
+            return [], ms, f"non-array response: {str(arr)[:120]}"
+        ids = [x.get("id") for x in arr if isinstance(x, dict) and x.get("id")]
+        return ids, ms, None
+
+    def stop(self):
+        """Kill and CONFIRM. A test process that outlives its test is a bug."""
+        if self.pid is None:
+            self.confirmed_dead = True
+            return True
+        for sig in (signal.SIGTERM, signal.SIGKILL):
+            try:
+                os.kill(self.pid, sig)
+            except ProcessLookupError:
+                break
+            except Exception:
+                pass
+            for _ in range(20):
+                try:
+                    os.kill(self.pid, 0)
+                except ProcessLookupError:
+                    break
+                time.sleep(0.1)
+            else:
+                continue
+            break
+        try:
+            self.proc.wait(timeout=5)
+        except Exception:
+            pass
+        try:
+            os.kill(self.pid, 0)
+            self.confirmed_dead = False
+        except ProcessLookupError:
+            self.confirmed_dead = True
+        if self.verbose:
+            print(f"  pid {self.pid}: {'CONFIRMED DEAD' if self.confirmed_dead else 'STILL ALIVE'}")
+        if self.home and os.path.isdir(self.home):
+            shutil.rmtree(self.home, ignore_errors=True)
+        return self.confirmed_dead
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# eval
+# ─────────────────────────────────────────────────────────────────────────────
+def evaluate(soul, gold, limit):
+    rows = []
+    for q in gold["queries"]:
+        ids, ms, err = soul.recall(q["query"], limit)
+        rel = q.get("relevant") or []
+        row = {
+            "id": q["id"],
+            "category": q["category"],
+            "query": q["query"],
+            "returned": ids,
+            "n_returned": len(ids),
+            "latency_ms": round(ms, 1),
+            "error": err,
+        }
+        if q.get("expect_empty"):
+            row["clean"] = (len(ids) == 0)
+            row["false_positives"] = len(ids)
+        else:
+            row["hit@5"] = hit_at_k(ids, rel, 5)
+            row["recall@5"] = recall_at_k(ids, rel, 5)
+            row["recall@10"] = recall_at_k(ids, rel, 10)
+            row["precision@5"] = precision_at_k(ids, rel, 5)
+            row["mrr@10"] = mrr(ids, rel, 10)
+        if q.get("must_outrank"):
+            correct, stale = q["must_outrank"]
+            ic = ids.index(correct) if correct in ids else None
+            istale = ids.index(stale) if stale in ids else None
+            # Correct must be present AND above the stale node. A run that
+            # returns neither is NOT a pass: the corrected fact is what the
+            # user needed.
+            row["outranks"] = (ic is not None) and (istale is None or ic < istale)
+            row["rank_correct"] = None if ic is None else ic + 1
+            row["rank_stale"] = None if istale is None else istale + 1
+        rows.append(row)
+    return rows
+
+
+def aggregate(rows):
+    scored = [r for r in rows if "hit@5" in r]
+    nonsense = [r for r in rows if "clean" in r]
+    outrank = [r for r in rows if "outranks" in r]
+    lat = sorted(r["latency_ms"] for r in rows)
+    agg = {
+        "n_queries": len(rows),
+        "n_scored": len(scored),
+        "hit@5": mean([r["hit@5"] for r in scored]),
+        "recall@5": mean([r["recall@5"] for r in scored]),
+        "recall@10": mean([r["recall@10"] for r in scored]),
+        "precision@5": mean([r["precision@5"] for r in scored]),
+        "mrr@10": mean([r["mrr@10"] for r in scored]),
+        "nonsense_clean": f"{sum(1 for r in nonsense if r['clean'])}/{len(nonsense)}",
+        "superseded_outranks": f"{sum(1 for r in outrank if r['outranks'])}/{len(outrank)}",
+        "latency_ms_p50": lat[len(lat) // 2] if lat else 0,
+        "latency_ms_p95": lat[max(0, int(len(lat) * 0.95) - 1)] if lat else 0,
+        "latency_ms_max": lat[-1] if lat else 0,
+        "errors": sum(1 for r in rows if r["error"]),
+        "by_category": {},
+    }
+    cats = sorted({r["category"] for r in rows})
+    for c in cats:
+        cr = [r for r in rows if r["category"] == c]
+        if c == "nonsense":
+            agg["by_category"][c] = {
+                "n": len(cr),
+                "clean": sum(1 for r in cr if r["clean"]),
+                "avg_false_positives": mean([float(r["false_positives"]) for r in cr]),
+            }
+        else:
+            e = {
+                "n": len(cr),
+                "hit@5": mean([r.get("hit@5") for r in cr]),
+                "recall@5": mean([r.get("recall@5") for r in cr]),
+                "recall@10": mean([r.get("recall@10") for r in cr]),
+                "mrr@10": mean([r.get("mrr@10") for r in cr]),
+            }
+            if c == "superseded":
+                e["outranks"] = sum(1 for r in cr if r.get("outranks"))
+            agg["by_category"][c] = e
+    return agg
+
+
+def print_table(label, agg):
+    print(f"\n=== {label} ===")
+    print(f"  queries {agg['n_queries']} ({agg['n_scored']} scored + "
+          f"{agg['n_queries'] - agg['n_scored']} control) · errors {agg['errors']}")
+    print(f"  {'hit@5':>12} {'recall@5':>10} {'recall@10':>10} {'prec@5':>9} {'MRR@10':>9}")
+    print(f"  {pct([agg['hit@5']]):>12} {pct([agg['recall@5']]):>10} {pct([agg['recall@10']]):>10} "
+          f"{pct([agg['precision@5']]):>9} {agg['mrr@10']:>9.3f}")
+    print(f"  nonsense clean {agg['nonsense_clean']} · superseded outranks {agg['superseded_outranks']}")
+    print(f"  latency ms  p50 {agg['latency_ms_p50']:.0f} · p95 {agg['latency_ms_p95']:.0f} "
+          f"· max {agg['latency_ms_max']:.0f}")
+    print(f"\n  {'category':14} {'n':>3} {'hit@5':>8} {'recall@5':>9} {'recall@10':>10} {'MRR@10':>8}")
+    for c, e in agg["by_category"].items():
+        if c == "nonsense":
+            print(f"  {c:14} {e['n']:>3} {'clean ' + str(e['clean']) + '/' + str(e['n']):>8}"
+                  f"{'':>9} {'':>10} {'avg FP ' + format(e['avg_false_positives'], '.1f'):>8}")
+        else:
+            extra = f"  outranks {e['outranks']}/{e['n']}" if "outranks" in e else ""
+            print(f"  {c:14} {e['n']:>3} {pct([e['hit@5']]):>8} {pct([e['recall@5']]):>9} "
+                  f"{pct([e['recall@10']]):>10} {e['mrr@10']:>8.3f}{extra}")
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument("--soul", required=True)
+    ap.add_argument("--corpus", required=True)
+    ap.add_argument("--label", required=True)
+    ap.add_argument("--gold", default=os.path.join(HERE, "gold_set.json"))
+    ap.add_argument("--port", type=int, default=7893)
+    ap.add_argument("--limit", type=int, default=10)
+    ap.add_argument("--out", default=None)
+    args = ap.parse_args()
+
+    with open(args.gold, encoding="utf-8") as fh:
+        gold = json.load(fh)
+    print(f"[{args.label}] soul={os.path.basename(args.soul)} "
+          f"corpus={os.path.basename(args.corpus)} gold={len(gold['queries'])}q limit={args.limit}")
+
+    soul = Soul(args.soul, args.corpus, args.port)
+    rows = []
+    started = time.time()
+    try:
+        soul.start()
+        rows = evaluate(soul, gold, args.limit)
+    finally:
+        dead = soul.stop()
+
+    agg = aggregate(rows)
+    print_table(args.label, agg)
+
+    out = args.out or os.path.join(HERE, f"results-{args.label}.json")
+    doc = {
+        "label": args.label,
+        "soul_binary": os.path.abspath(args.soul),
+        "soul_md5": subprocess.run(["md5", "-q", args.soul], capture_output=True,
+                                   text=True).stdout.strip(),
+        "corpus": os.path.abspath(args.corpus),
+        "corpus_nodes": gold.get("corpus_nodes"),
+        "corpus_edges": gold.get("corpus_edges"),
+        "gold_set": os.path.abspath(args.gold),
+        "limit": args.limit,
+        "port": args.port,
+        "wall_clock_s": round(time.time() - started, 1),
+        "child_pid": soul.pid,
+        "child_confirmed_dead": soul.confirmed_dead,
+        "aggregate": agg,
+        "rows": rows,
+    }
+    with open(out, "w", encoding="utf-8") as fh:
+        json.dump(doc, fh, indent=1, ensure_ascii=False)
+    print(f"\nwrote {out}")
+    if not dead:
+        print("FATAL: child process could not be confirmed dead", file=sys.stderr)
+        sys.exit(4)
+
+
+if __name__ == "__main__":
+    main()

tools/retrieval-eval/sim-bm25.py

@@ -0,0 +1,142 @@
+import numpy as np, json, urllib.request, collections, math, re, sys, time
+SP="/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad"
+EV="/Users/timlingo/Development/neuron-technologies/_wt-semseed/tools/retrieval-eval/"
+np.seterr(all='ignore')
+t0=time.time()
+M=np.load(SP+'/emb.npy'); eids=open(SP+'/ids.txt',encoding='utf-8',errors='surrogateescape').read().split('\n')
+eidx={k:i for i,k in enumerate(eids)}
+d=json.load(open('/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json',encoding='utf-8',errors='surrogateescape'))
+print("loaded corpus %.1fs"%(time.time()-t0),file=sys.stderr)
+STRUCT={"identity","contains","superseded_by","references","embodies","demonstrated_by","canonical-self","depends_on","currently_holds","activates"}
+adj=collections.defaultdict(list)
+for e in d['edges']:
+    if e.get('relation') not in STRUCT: continue
+    w=float(e.get('weight') or 0.0)
+    adj[e['from_id']].append((e['to_id'],w)); adj[e['to_id']].append((e['from_id'],w))
+nodes=d['nodes']
+N={n['id']:n for n in nodes}
+PRINT=re.compile(r'^[\x20-\x7e]+$')
+ids=[]; hay=[]; dl=[]; sal=[]; addressable=[]
+for n in nodes:
+    i=n.get('id') or ''
+    h=((n.get('content') or '')+'\x00'+(n.get('label') or '')+'\x00'+(n.get('tags') or '')).lower()
+    ids.append(i); hay.append(h); dl.append(len(h)); sal.append(float(n.get('salience') or 0.0))
+    addressable.append(bool(PRINT.match(i)))
+del d
+NN=len(ids); avgdl=sum(dl)/NN
+print("nodes=%d avgdl=%.0f addressable=%d  %.1fs"%(NN,avgdl,sum(addressable),time.time()-t0),file=sys.stderr)
+gold={q['id']:q for q in json.load(open(EV+"gold_set.json"))['queries']}
+LEXMAIN={r['id']:r['returned'] for r in json.load(open(EV+"results-main.json"),) ['rows']} if False else {r['id']:r['returned'] for r in json.load(open(EV+"results-main.json",encoding='utf-8',errors='surrogateescape'))['rows']}
+CACHE={}
+def emb(t):
+    if t in CACHE: return CACHE[t]
+    b=json.dumps({"model":"nomic-embed-text","prompt":t}).encode()
+    r=urllib.request.Request("http://127.0.0.1:11434/api/embeddings",data=b,headers={"Content-Type":"application/json"})
+    v=np.array(json.load(urllib.request.urlopen(r,timeout=60))["embedding"],dtype=np.float32)
+    v=v/(np.linalg.norm(v)+1e-9); CACHE[t]=v; return v
+K1,B=1.2,0.75
+def lexleg(query, mode, guard, lim=10):
+    toks=[]
+    for w in query.split():
+        wl=w.lower()
+        if wl not in toks: toks.append(wl)
+    nt=len(toks)
+    masks=[]; df=[0]*nt
+    for i in range(NN):
+        if guard and not addressable[i]: continue
+        h=hay[i]; m=0; sc=0
+        for t in range(nt):
+            if toks[t] in h: m|=(1<<t); sc+=1; df[t]+=1
+        if sc: masks.append((i,m,sc))
+    if mode=='tokcount':
+        masks.sort(key=lambda x:(-x[2], -sal[x[0]]))
+        return [ids[i] for i,m,sc in masks[:lim]]
+    idf=[math.log(1.0+(NN-df[t]+0.5)/(df[t]+0.5)) for t in range(nt)]
+    scored=[]
+    for i,m,sc in masks:
+        norm=1.0-B+B*dl[i]/avgdl
+        s=0.0
+        for t in range(nt):
+            if m&(1<<t): s+=idf[t]*(K1+1.0)/(1.0+K1*norm)
+        scored.append((s,i))
+    scored.sort(key=lambda x:(-x[0], -sal[x[1]]))
+    return [ids[i] for s,i in scored[:lim]]
+FIRE=0.02; DECAY=0.7; DEPTH=2; SEED_MIN=0.60; ASSOC_MAX=64
+def assoc(seeds, s):
+    act={x:1.0 for x in seeds}; seen={x:2 for x in seeds}
+    Q=[(x,0) for x in seeds]; h=0
+    while h<len(Q):
+        cur,hop=Q[h]; h+=1
+        if hop>=DEPTH: continue
+        p=act[cur]
+        for oid,w in adj.get(cur,()):
+            n=N.get(oid)
+            if not n or n.get('node_type') in ('Tag','InternalStateEvent'): continue
+            na=p*w*DECAY*float(n.get('salience') or 0.0)
+            if na<FIRE: continue
+            if oid in seen and na<=act.get(oid,0): continue
+            act[oid]=na
+            if oid not in seen: seen[oid]=1
+            Q.append((oid,hop+1))
+    out=[]
+    for k,v in seen.items():
+        if v!=1 or k not in eidx: continue
+        c=float(s[eidx[k]])
+        if c<=0: continue
+        out.append((c,k))
+    out.sort(reverse=True)
+    return [k for c,k in out[:ASSOC_MAX]]
+def inter3(L,S,A,lim=10):
+    out=[]; li=si=ai=0
+    while len(out)<lim and (li<len(L) or si<len(S) or ai<len(A)):
+        if li<len(L):
+            if L[li] not in out: out.append(L[li])
+            li+=1
+        if len(out)>=lim: break
+        if si<len(S):
+            if S[si] not in out: out.append(S[si])
+            si+=1
+        if len(out)>=lim: break
+        if ai<len(A):
+            if A[ai] not in out: out.append(A[ai])
+            ai+=1
+    return out
+def run(mode, guard, use_main_lex=False):
+    res={}; legs={}
+    for qid,q in gold.items():
+        v=emb(q['query']); s=M@v; s[~np.isfinite(s)]=-1
+        L = LEXMAIN[qid][:10] if use_main_lex else lexleg(q['query'], mode, guard)
+        ordr=np.argsort(-s)
+        S=[eids[j] for j in ordr[:10] if s[j]>SEED_MIN]
+        if guard: S=[x for x in S if PRINT.match(x or '')]
+        seeds=[x for x in L[:3] if x in N]
+        seeds=seeds+[eids[j] for j in ordr[:8] if eids[j] in N and eids[j] not in seeds and (not guard or PRINT.match(eids[j] or ''))]
+        A=assoc(seeds,s) if seeds else []
+        if guard: A=[x for x in A if PRINT.match(x or '')]
+        res[qid]=inter3(L,S,A); legs[qid]=(L,S,A)
+    return res,legs
+def score(res,label,verbose=False):
+    det={}
+    for qid,q in gold.items():
+        out=res[qid][:5]
+        if q['category']=='nonsense': ok=(len(res[qid])==0)
+        elif q['category']=='superseded':
+            must=q.get('must_outrank') or {}; ok=False
+            for good,bad in (must.items() if isinstance(must,dict) else []):
+                ok = good in res[qid] and (bad not in res[qid] or res[qid].index(good)<res[qid].index(bad))
+            if not must: ok=any(r in out for r in q['relevant'])
+        else: ok=any(r in out for r in q['relevant'])
+        det[qid]=ok
+    print("%-28s outcome-true=%d/38"%(label,sum(det.values())))
+    return det
+if __name__=="__main__":
+    base,_=run('tokcount',False,use_main_lex=True); b=score(base,'BASELINE semseed(real lex)')
+    variants=[('tokcount',False,'replica: tokcount,noguard'),
+              ('tokcount',True ,'A: tokcount + idguard'),
+              ('bm25',    False,'B: bm25 only'),
+              ('bm25',    True ,'C: bm25 + idguard')]
+    dets={}
+    for m,g,lab in variants:
+        r,_=run(m,g); dets[lab]=score(r,lab)
+        dd=[q for q in gold if dets[lab][q]!=b[q]]
+        print("     vs BASELINE moved=%d gains=%s losses=%s"%(len(dd),[q for q in dd if dets[lab][q]],[q for q in dd if not dets[lab][q]]))

tools/retrieval-eval/wb2.py

@@ -0,0 +1,92 @@
+import json,sys,pickle,numpy as np
+sys.path.insert(0,'.')
+from legs import *
+GP='/Users/timlingo/Development/neuron-technologies/_wt-bm25lex/tools/retrieval-eval/'
+G=json.load(open(GP+'gold_set.json'))
+def wstart(s,tok):
+    i=s.find(tok)
+    while i!=-1:
+        if i==0 or not s[i-1].isalnum(): return True
+        i=s.find(tok,i+1)
+    return False
+def legs4(query, wordstart=False, unfloor=False):
+    toks=tokenize(query); lt=[t.lower() for t in toks]
+    hit_idx=[];hit_mask=[];df=[0]*len(toks)
+    for i in range(N):
+        if not OK[i]: continue
+        s=LOW[i];m=0
+        for t,tok in enumerate(lt):
+            if tok in s and (not wordstart or wstart(s,tok)): m|=(1<<t)
+        if m:
+            hit_idx.append(i);hit_mask.append(m)
+            for t in range(len(toks)):
+                if m>>t&1: df[t]+=1
+    dl_n=int(OK.sum());avgdl=float(DL[OK].sum()/max(dl_n,1))
+    idf=[math.log(1.0+((dl_n-d+0.5)/(d+0.5))) for d in df]
+    L=[]
+    for j,i in enumerate(hit_idx):
+        norm=1.0-B+B*(DL[i]/avgdl);w=0.0
+        for t in range(len(toks)):
+            if hit_mask[j]>>t&1: w+=idf[t]*(K1+1.0)/(1.0+K1*norm)
+        L.append((i,w,SAL[i]))
+    L.sort(key=lambda x:(-x[1],-x[2]))
+    if not L: return [],[],[]
+    qv=qemb(query);cos=En@qv;cos=np.where(HAVE&OK,cos,-2.0)
+    order=np.argsort(-cos)[:600]
+    Sl=[int(i) for i in order if cos[i]>(0.0 if unfloor else SEED_MIN)]
+    semseed=[int(i) for i in order[:SEED_K] if cos[i]>0.0]
+    act={};seen={};qq=[]
+    for i,_,_ in L[:ASSOC_SEEDS]:
+        act[i]=1.0;seen[i]=2;qq.append((i,0))
+    for i in semseed:
+        if i in seen: continue
+        act[i]=1.0;seen[i]=2;qq.append((i,0))
+    qh=0
+    while qh<len(qq):
+        cur,h=qq[qh];qh+=1
+        if h>=DEPTH: continue
+        parent=act[cur]
+        for e,oi in ADJ_F[cur]+ADJ_T[cur]:
+            if e['rel'] not in STRUCT or EXCL[oi]: continue
+            na=parent*e['w']*DECAY*SAL[oi]
+            if na<FIRE: continue
+            if seen.get(oi) and na<=act.get(oi,0): continue
+            act[oi]=na
+            if not seen.get(oi): seen[oi]=1
+            if len(qq)<AMAX*4: qq.append((oi,h+1))
+    A=sorted([(i,float(cos[i])) for i,st in seen.items() if st==1 and OK[i] and HAVE[i] and cos[i]>0.0],key=lambda x:-x[1])[:AMAX]
+    return [i for i,_,_ in L],Sl,[i for i,_ in A]
+def merge(L,S,A,lim=10):
+    out=[];li=si=ai=0
+    while len(out)<lim and (li<len(L) or si<len(S) or ai<len(A)):
+        if li<len(L):
+            if L[li] not in out: out.append(L[li])
+            li+=1
+        if len(out)>=lim: break
+        if si<len(S):
+            if S[si] not in out: out.append(S[si])
+            si+=1
+        if len(out)>=lim: break
+        if ai<len(A):
+            if A[ai] not in out: out.append(A[ai])
+            ai+=1
+    return out
+def outcome(q,ids):
+    c=q['category']
+    if c=='nonsense': return len(ids)==0
+    if c=='superseded':
+        a,b=q['must_outrank']
+        if a not in ids: return False
+        if b not in ids: return True
+        return ids.index(a)<ids.index(b)
+    return any(x in ids[:5] for x in q['relevant'])
+def run(**kw):
+    return {q['id']:outcome(q,[NODES[i]['id'] for i in merge(*legs4(q['query'],**kw),10)]) for q in G['queries']}
+base=run()
+print("baseline",sum(base.values()),"misses",[k for k,v in base.items() if not v])
+for name,kw in [('wordstart',dict(wordstart=True)),
+                ('unfloor',dict(unfloor=True)),
+                ('wordstart+unfloor',dict(wordstart=True,unfloor=True))]:
+    r=run(**kw)
+    g=sorted(k for k in base if r[k] and not base[k]);l=sorted(k for k in base if base[k] and not r[k])
+    print("%-20s net=%+d gains=%s losses=%s"%(name,len(g)-len(l),g,l))

tools/retrieval-eval/zprobe.py

@@ -0,0 +1,31 @@
+import numpy as np, json, urllib.request
+SP="/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad"
+M=np.load(SP+'/emb.npy'); ids=open(SP+'/ids.txt',encoding='utf-8',errors='surrogateescape').read().split('\n')
+np.seterr(all='ignore')
+bad=~np.isfinite(M).all(axis=1)
+M[bad]=0.0
+print("non-finite rows zeroed:",int(bad.sum()))
+idx={k:i for i,k in enumerate(ids)}
+gold=json.load(open("/Users/timlingo/Development/neuron-technologies/_wt-assoc-leg/tools/retrieval-eval/gold_set.json"))['queries']
+def emb(t):
+    b=json.dumps({"model":"nomic-embed-text","prompt":t}).encode()
+    r=urllib.request.Request("http://127.0.0.1:11434/api/embeddings",data=b,headers={"Content-Type":"application/json"})
+    v=np.array(json.load(urllib.request.urlopen(r,timeout=60))["embedding"],dtype=np.float32)
+    return v/(np.linalg.norm(v)+1e-9)
+out={}
+for q in gold:
+    v=emb(q['query']); s=M@v
+    s=s[np.isfinite(s)]
+    mu=float(s.mean()); sd=float(s.std())
+    top=np.sort(s)[::-1][:10]
+    z=[(float(t)-mu)/sd for t in top]
+    grank=[]
+    for rel in q['relevant']:
+        if rel in idx:
+            j=idx[rel]; grank.append((int((M@v > (M@v)[j]).sum())+1, round(float((M@v)[j]),3)))
+    grank.sort()
+    out[q['id']]=dict(cat=q['category'],mu=round(mu,3),sd=round(sd,4),top1=round(float(top[0]),3),
+                      z1=round(z[0],2),z3=round(z[2],2),z5=round(z[4],2),gold=grank[:1])
+    print("%s %-11s mu=%.3f sd=%.4f top1=%.3f z1=%5.2f z3=%5.2f z5=%5.2f gold=%s"%(
+        q['id'],q['category'],mu,sd,top[0],z[0],z[2],z[4],grank[:1]))
+json.dump(out,open(SP+'/zprobe.json','w'),indent=1)