chore(engine): deploys build from the committed input, not a second lineage

Until now deploys were built by build-soul.sh from a scratch amalgam while CI
compiled the committed dist/soul.c. Two lineages — 'what runs' and 'what the repo
says builds' were different artifacts. That is #133/#111 in another costume, and it
is how a round-9.1 brain shipped matching no committed source at all.

build-soul-from-dist.sh asserts dist/soul.c matches the .el sources, compiles it
with CI's own flags (-O2 -DHAVE_CURL -rdynamic; the CI comment explains -rdynamic —
without it the runtime cannot resolve its HTTP handler by name and the binary serves
nothing on every route), and writes a .provenance sidecar recording the dist/soul.c
hash, the stamp hash and the commit.

deploy_binary.sh gains GATE 0: refuse any soul without provenance, or built from a
dist/soul.c other than the one in the repo now. The override
(NEURON_DEPLOY_UNSTAMPED=i-accept-two-lineages) exists deliberately — a gate with no
escape hatch gets bypassed by disabling the gate, which is worse than one that
announces itself.

Verified before enforcing, so the sanctioned path is not a broken one:
  interface parity with the deployed binary   108 routes in, 108 out
  boots and serves                            2s
  carries today's work                        24 self-neighbours, 17 identity records
  GATE 0 refuses an unstamped binary          exit 10
  GATE 0 accepts the stamped one, deployed    durability PASS

Production now runs 4845db3d, built from dist/soul.c at 9fd8c11. After the swap:
identity in context 17, connections still form on write, semantic recall intact,
mind and store at delta 0.

Refs #133, #111

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

.gitea/workflows/ci.yaml

@@ -63,6 +63,16 @@ jobs:
           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/)"
 
+      # 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: |
           RUNTIME=/opt/el/runtime

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.el

@@ -1162,7 +1162,7 @@ fn hist_trim_with_bell_guard(hist: String) -> String {
             + " | evicted_at:" + ts_str
             + " | message:" + safe_content
         let preserve_tags: String = "[\"bell-history\",\"bell:" + bell_level + "\",\"evicted\",\"affective\",\"BellEvent\"]"
-        let discard: String = engram_node_full(
+        let discard: String = wt_node(
             preserve_content,
             "BellEvent",
             "bell:" + bell_level + ":preserved",
@@ -1210,7 +1210,7 @@ fn conv_history_persist(session_id: String, hist: String) -> Void {
     if !str_contains(hist, "]") { return "" }
     let tags: String = "[\"conv-history\",\"persistent\"]"
     // FIX B: one label rule, shared with the agentic path. See conv_hist_label.
-    let node_id: String = engram_node_full(
+    let node_id: String = wt_node(
         hist, "Conversation", conv_hist_label(session_id),
         el_from_float(0.7), el_from_float(0.8), el_from_float(0.9),
         "Episodic", tags
@@ -3461,7 +3461,7 @@ fn handle_dharma_room_turn(body: String) -> String {
     // engram_node(content, "episodic", ...) which wrongly put a TIER into the node_type
     // slot — that's why nodes showed node_type="episodic". Use the full, correct contract.)
     let utterance_tags: String = "[\"soul-utterance\",\"episodic\"]"
-    let discard_id: String = engram_node_full(
+    let discard_id: String = wt_node(
         clean_response, "Conversation", "soul:utterance",
         el_from_float(0.6), el_from_float(0.6), el_from_float(0.8),
         "Episodic", utterance_tags
@@ -3552,7 +3552,7 @@ fn session_summary_write(summary_text: String) -> String {
         }
     }
     let tags: String = "[\"SessionSummary\",\"session-summary\",\"previous-session\",\"consolidate\"]"
-    let node_id: String = engram_node_full(
+    let node_id: String = wt_node(
         content, "SessionSummary", "session:summary",
         el_from_float(0.85), el_from_float(0.85), el_from_float(1.0),
         "Episodic", tags
@@ -3578,7 +3578,7 @@ fn session_summary_write_dated(summary_text: String, label: String) -> String {
     let ts_str: String = int_to_str(ts)
     let content: String = "[session-summary] " + trimmed + " | ts:" + ts_str
     let tags: String = "[\"SessionSummary\",\"session-summary\",\"previous-session\",\"consolidate\"]"
-    let node_id: String = engram_node_full(
+    let node_id: String = wt_node(
         content, "SessionSummary", label,
         el_from_float(0.9), el_from_float(0.8), el_from_float(1.0),
         "Episodic", tags
@@ -3654,7 +3654,7 @@ fn auto_persist(req: String, resp: String) -> Void {
         + ",\"bell\":\"" + bell_level + "\""
         + ",\"label\":\"chat:" + ts_str + "\"}"
 
-    let conv_node_id: String = engram_node_full(
+    let conv_node_id: String = wt_node(
         content,
         "Conversation",
         "chat:" + ts_str,
@@ -3692,7 +3692,7 @@ fn auto_persist(req: String, resp: String) -> Void {
         let bell_tags: String = "[\"safety\",\"bell\",\"bell:" + bell_level + "\",\"affective\",\"BellEvent\"]"
         let bell_ts_str: String = int_to_str(time_now())
         let bell_label: String = "bell:" + bell_level + ":" + bell_ts_str
-        let bell_node_id: String = engram_node_full(
+        let bell_node_id: String = wt_node(
             bell_content,
             "BellEvent",
             bell_label,
@@ -3751,7 +3751,7 @@ fn auto_persist(req: String, resp: String) -> Void {
         let pos_tags: String = "[\"joy\",\"positive\",\"joy:" + positive_level + "\",\"affective\",\"PositiveEvent\"]"
         let pos_ts_label: String = int_to_str(time_now())
         let pos_label: String = "joy:" + positive_level + ":" + pos_ts_label
-        let pos_node_id: String = engram_node_full(
+        let pos_node_id: String = wt_node(
             pos_content, "PositiveEvent", pos_label,
             pos_sal_a, pos_sal_b, pos_sal_c, "Episodic", pos_tags
         )

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 e31f760de5f6629cd37bcfd26172f92be3ca5d6ff36480f6adafa1d4a1de5a66
+# generated_amalgam_bytes  1179122
+f8597e10546654bce3fbbe40461b2da59d0e06dbf1b038d1d362d24f949e3911  awareness.el
+b6f3d14ca0c26017a2d617399a6d3754dabb0905e4d5f52eb75d25c4ad18d3c5  chat.el
+42288c212cbf72fb1e8ecbd4d9900e4e9ee1cfa475b7974295c7637f1bf2939f  elp-input.el
+b3f77f49d6086932c38bd17fe7a5eaf8bce25685f6fc3e1750f05729c6b49b9e  imprint.el
+fba8ffdb9ba72bca5b09ca1c93a520edc52f3f4d8aec2c7585fe9b17e06420b2  manifest.el
+550a72e234ae8cec1f33e02108fd365353f45edd88513da90b792e79b6c0e5f0  memory.el
+77640783df5c38066149dcd11a11aea7e36f66e40e3df6aedf6723be8b9e0e1e  neuron-api.el
+03c47c451e0e87f2c252cadb4b765867943962a804f548dd53adeef0520912c8  persist.el
+541b9309c59c33ee619d393714871b820ec4151b721d8b2aebcfdb7ce8eb2ffa  routes.el
+c28e36952ec56525963a0bdf29455ab097d3b0c5653d19c25fbb005e1069a1f7  safety.el
+fd3ab91d0ae0ea26639e21bef2f8f94054dc4b02eae68b19e3fe689d2769aad4  sessions.el
+0f1cf43904a98a5a646cce5a07e0e96162ced662692fbc13357d9b67d9a8ac3d  soul.el
+30337940905171a9645b0929f0a412ce6b3dccb1246495070c553bca0bbae6cd  stewardship.el
+e105dc5990e6adbf39db9dc0462cd8bcf6e6c3dfd03709059227ecfad2bbab29  studio.el

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

@@ -195,15 +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.
@@ -295,10 +304,35 @@ fn handle_api_begin_session(body: String) -> String {
     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 + "}"
 }
 
@@ -342,10 +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}"
 }
 
@@ -369,7 +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) }
@@ -422,11 +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}"
 }
 
@@ -450,7 +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)
 }
 
@@ -498,7 +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) }
@@ -513,12 +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}"
 }
@@ -535,11 +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 + "\"}"
 }
 
@@ -562,7 +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) }
@@ -647,7 +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) }
@@ -694,7 +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 + "\"}"
 }
 
@@ -727,11 +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}"
 }
@@ -789,11 +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}"
     }
@@ -809,11 +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}"
     }
@@ -833,7 +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}"
     }
 
@@ -868,7 +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),

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

@@ -186,7 +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",
@@ -208,7 +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",
@@ -239,7 +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",
@@ -395,7 +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 —
@@ -432,10 +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")

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,

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

soul.el

@@ -657,6 +657,23 @@ 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")

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,

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/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,
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+}

tools/retrieval-eval/cmp-splitfix.json

@@ -0,0 +1,149 @@
+{
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+}

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

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

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

@@ -0,0 +1,166 @@
+{
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+ "verdict": "candidate better",
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+}

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

@@ -0,0 +1,155 @@
+{
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+ "fixed_by_candidate": [
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+ "min_detectable_swing_queries": 6,
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+ "verdict": "no measurable difference",
+ "baseline_aggregate": {
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+    "recall@10": 1.0,
+    "mrr@10": 1.0
+   },
+   "heldout_paraphrase": {
+    "n": 30,
+    "hit@5": 0.16666666666666666,
+    "recall@5": 0.16666666666666666,
+    "recall@10": 0.26666666666666666,
+    "mrr@10": 0.0762037037037037
+   },
+   "nonsense": {
+    "n": 10,
+    "clean": 10,
+    "avg_false_positives": 0.0
+   },
+   "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": 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
+   }
+  }
+ },
+ "repeat_variance": {}
+}

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/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/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/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-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",
+ "corpus_nodes": 78768,
+ "corpus_edges": 14214,
+ "gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
+ "limit": 10,
+ "port": 7895,
+ "wall_clock_s": 28.7,
+ "child_pid": 1490,
+ "child_confirmed_dead": true,
+ "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": "3/3",
+  "superseded_outranks": "2/3",
+  "latency_ms_p50": 537.6,
+  "latency_ms_p95": 733.7,
+  "latency_ms_max": 761.4,
+  "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": 3,
+    "avg_false_positives": 0.0
+   },
+   "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
+   }
+  }
+ },
+ "rows": [
+  {
+   "id": "q01",
+   "category": "exact_rare",
+   "query": "unjailbreakable",
+   "returned": [
+    "mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226"
+   ],
+   "n_returned": 1,
+   "latency_ms": 165.0,
+   "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",
+    "bl-ba764d70-e9d7-4f62-848f-719cb665f45e",
+    "mem-22fe5ec8-ae0d-4583-a05c-d1ef50353257",
+    "bl-b28d7256-6f74-4567-bd90-40d0ef2a6d78",
+    "project-engram",
+    "ctx-45bc",
+    "project-engram-lang",
+    "ctx-175f",
+    "mem-60778715-758c-4677-933d-fc39b8f94152",
+    "ctx-74ed"
+   ],
+   "n_returned": 10,
+   "latency_ms": 164.5,
+   "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": 163.7,
+   "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": 172.2,
+   "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",
+    "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_"
+   ],
+   "n_returned": 3,
+   "latency_ms": 167.0,
+   "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"
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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": [
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
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+    "knw-f671966c-3387-4848-abca-b5deec122e00",
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+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
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+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6"
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+   "mrr@10": 1.0
+  },
+  {
+   "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",
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+    "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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+   "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",
+   "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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+   "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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+   "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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+  },
+  {
+   "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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+    "mem-a535f205-bc4c-4058-9171-6263c496044a",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "mem-0228da71-d7f7-4f3b-b7b3-c5eede42b62a",
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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",
+    "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
+    "7452eb8f-be01-4b55-aec1-ff0c29e790f6",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "532277bf-2959-4beb-ae0d-b018c97678ee",
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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",
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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",
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+    "mem-75e490d1-f0a9-4b73-8cfc-8daecfaf6f38",
+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
+    "a1000001-0000-0000-0000-000000000010",
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+    "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",
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+    "a708dd6e-fe73-4f2f-a21e-89daa0985487",
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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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+    "knw-12b4b913-7a25-4b0d-844c-504c01d6725e",
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+    "knw-9707256e-ed44-4042-bd88-f90fa514e1cf",
+    "34356a36-0df5-4020-8dcc-5e7a423f8d4c",
+    "knw-0087493b-25cd-45b0-bf46-c078c5b49718",
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+   "precision@5": 0.2,
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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",
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+  {
+   "id": "q25",
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+   "query": "cheerfulness you arrive at instead of assuming",
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+    "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
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+  {
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+  },
+  {
+   "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",
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+  {
+   "id": "q28",
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+    "54608b69-78b6-4239-b60f-b8206cfecacc",
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+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
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+  {
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+   "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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+   "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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+    "kn-6f248a50-355b-47bb-aec8-e0e646a9b077",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "mem-ab34c2f7-3243-424b-affa-25555f6cf9cc"
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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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+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
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+   "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",
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+    "knw-473f3f24-20f6-4f39-8589-3709538eb6ac",
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+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
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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",
+    "tag-__darma____cgi____patents____self-improvement____character-preservation____autonomous____kotlin____architecture__",
+    "knw-e047bb42-dc5b-4383-9e88-e508dc03abe3",
+    "mem-c17aefb1-38b5-4ced-af50-fe524127e1a4",
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+    "bl-145a0985-2382-400f-a7c5-c335c5e30a72",
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+   "rank_correct": 2,
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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",
+    "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"
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+  },
+  {
+   "id": "q38",
+   "category": "superseded",
+   "query": "is MCP still the live integration layer",
+   "returned": [
+    "5fcba804-eb5b-48ec-82da-146b1c6bb50d",
+    "bl-7328cbe3-0200-43c2-88e7-0a164e15fca4",
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+    "bl-c5c6571e-118f-47c7-8cbb-3ed0ebf64a51",
+    "mem-101e81b4-8097-4749-8d8d-7bb66de34517",
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+    "bl-4f7b651b-6b33-449c-8a3b-cfce12ce984b",
+    "mem-3a2cf162-d93b-4f29-86f2-5066fb7fe1f5"
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+   "rank_correct": null,
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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,
+ "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": 28.9,
+ "child_pid": 1420,
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+ "rows": [
+  {
+   "id": "q01",
+   "category": "exact_rare",
+   "query": "unjailbreakable",
+   "returned": [
+    "mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226"
+   ],
+   "n_returned": 1,
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q02",
+   "category": "exact_rare",
+   "query": "engram-migrate",
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+    "bl-ba764d70-e9d7-4f62-848f-719cb665f45e",
+    "mem-22fe5ec8-ae0d-4583-a05c-d1ef50353257",
+    "bl-b28d7256-6f74-4567-bd90-40d0ef2a6d78",
+    "project-engram",
+    "ctx-45bc",
+    "project-engram-lang",
+    "ctx-175f",
+    "mem-60778715-758c-4677-933d-fc39b8f94152",
+    "ctx-74ed"
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q03",
+   "category": "exact_rare",
+   "query": "cartabandonedevent",
+   "returned": [
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+  },
+  {
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+   "query": "pre-apprenticeship",
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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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+   "n_returned": 3,
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+   "mrr@10": 1.0
+  },
+  {
+   "id": "q06",
+   "category": "exact_rare",
+   "query": "clear-eyed",
+   "returned": [
+    "knw-c72597c5-c23d-4c08-8e9e-996dadf26a99"
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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": [
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "knw-7902acca-604e-409b-8faf-ad85424211d0",
+    "knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
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+    "knw-f671966c-3387-4848-abca-b5deec122e00",
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+    "knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
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+    "knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6"
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+   "mrr@10": 1.0
+  },
+  {
+   "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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+   "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": [
+    "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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+   "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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+   "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",
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+    "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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+  },
+  {
+   "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",
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+    "mem-434be7c8-88cb-4039-b79a-1da4ac4de783",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "a708dd6e-fe73-4f2f-a21e-89daa0985487",
+    "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",
+    "015644f5-8194-4af0-800d-dd4a0cd71396",
+    "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",
+    "kn-f230b362-b201-4402-9833-4160c89ab3d4",
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+    "mem-92a7fdc5-9dd0-48cf-a691-506058de3838",
+    "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",
+    "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
+    "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",
+    "bl-34f51ddb-a840-459f-a248-94214f5febb6",
+    "bl-286b562a-5299-40e0-a32a-afa9cbdfe995"
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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": [
+    "knw-723551f5-1950-42a3-8b89-b6a06913cef0",
+    "kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
+    "bl-4c5b385e-135a-4663-8521-96af0b491121",
+    "knw-12b4b913-7a25-4b0d-844c-504c01d6725e",
+    "bl-2b00aeb0-c0fa-4a9f-8f30-4207e98b3d52",
+    "knw-9707256e-ed44-4042-bd88-f90fa514e1cf",
+    "34356a36-0df5-4020-8dcc-5e7a423f8d4c",
+    "knw-0087493b-25cd-45b0-bf46-c078c5b49718",
+    "mem-22f5f665-3ad2-4063-88b0-915849a795f5",
+    "kn-0bb4f021-56de-4947-a35b-a37209e7ba21"
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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": [
+    "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",
+    "mem-5708f4c9-3d61-4182-8543-2843698931e6"
+   ],
+   "n_returned": 10,
+   "latency_ms": 634.6,
+   "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": [
+    "077d064f-3489-4c05-9aca-3782f96b51db",
+    "knw-f9ce17a7-17fc-431f-8f23-695b670ec4fa",
+    "kn-6061318f-046b-4935-907d-8eafdce14930",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "27e1b1a4-ad0b-49d9-812f-fedf43b8aabe",
+    "kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
+    "bl-87c93185-b2bf-40af-ae23-3c830c007abf",
+    "knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
+    "fce2792a-53fc-4d4a-be3b-42bd6ceb1ba7",
+    "a1000001-0000-0000-0000-000000000001"
+   ],
+   "n_returned": 10,
+   "latency_ms": 674.2,
+   "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": [
+    "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"
+   ],
+   "n_returned": 10,
+   "latency_ms": 571.6,
+   "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": [
+    "mem-b99efff0-00e6-40c8-9c5b-730330eef33b",
+    "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
+    "knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
+    "knw-f6ed7d00-bf7d-42ce-9e40-77cf3406e918",
+    "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/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/soulc-stamp.sh

@@ -0,0 +1,83 @@
+#!/usr/bin/env bash
+# soulc-stamp.sh — make it impossible for dist/soul.c to drift from the sources
+# in silence.
+#
+# THE PROBLEM (neuron#133, and its own words): "Nothing in the tree regenerates
+# this file. Only a human running the recipe. It lags in batches, never
+# per-change, and it will drift again."
+#
+# It drifted. On 2026-08-07 a CI or GKE 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. CI compiles dist/soul.c, not the .el files, so
+# the source being right is not the same as the build being right.
+#
+# WHY A STAMP AND NOT AUTO-REGENERATION: the CI workflow says elc cannot run on
+# the runner ("elb on Linux would OOM the runner (elc uses 24GB+ virtual memory
+# on a 16GB host)"). So the build cannot regenerate the file itself. What it CAN
+# do, for free and with no compiler, is refuse to compile a stale one.
+#
+# The stamp records a fingerprint of every .el source that feeds the amalgam at
+# the moment it was generated. --check recomputes and compares. Divergence is a
+# build failure with the recipe in the message, not a silent ship.
+#
+#   soulc-stamp.sh --write   after regenerating dist/soul.c (records the fingerprint)
+#   soulc-stamp.sh --check   in CI, before the compile (fails on drift)
+set -u
+MODE="${1:---check}"
+ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+STAMP="$ROOT/dist/soul.c.stamp"
+AMALGAM="$ROOT/dist/soul.c"
+
+# Every .el at the repo root is an input to the amalgam. Sorted so the hash is
+# order-independent; content-only so timestamps and checkouts do not perturb it.
+fingerprint() {
+  (
+    cd "$ROOT" || exit 1
+    for f in $(ls -1 *.el 2>/dev/null | sort); do
+      printf '%s  %s\n' "$(shasum -a 256 "$f" | awk '{print $1}')" "$f"
+    done
+  )
+}
+
+case "$MODE" in
+  --write)
+    [ -f "$AMALGAM" ] || { echo "no dist/soul.c to stamp — regenerate it first" >&2; exit 2; }
+    {
+      echo "# soul.c.stamp — fingerprint of the .el sources dist/soul.c was generated from."
+      echo "# Written by tools/soulc-stamp.sh --write. Do not hand-edit."
+      echo "# generated_amalgam_sha256 $(shasum -a 256 "$AMALGAM" | awk '{print $1}')"
+      echo "# generated_amalgam_bytes  $(wc -c < "$AMALGAM" | tr -d ' ')"
+      fingerprint
+    } > "$STAMP"
+    echo "stamped $(fingerprint | wc -l | tr -d ' ') sources -> dist/soul.c.stamp"
+    ;;
+
+  --check)
+    if [ ! -f "$STAMP" ]; then
+      echo "FAIL: dist/soul.c.stamp is missing — the build input is unverifiable." >&2
+      echo "      Regenerate the amalgam, then: tools/soulc-stamp.sh --write" >&2
+      exit 1
+    fi
+    RECORDED="$(grep -v '^#' "$STAMP")"
+    CURRENT="$(fingerprint)"
+    if [ "$RECORDED" = "$CURRENT" ]; then
+      echo "soulc-stamp: OK — dist/soul.c matches the .el sources"
+      exit 0
+    fi
+    echo "FAIL: dist/soul.c is STALE. It does not match the current .el sources." >&2
+    echo "" >&2
+    echo "CI compiles dist/soul.c, not the .el files. Shipping this means shipping" >&2
+    echo "an engine that does not contain the merged source. That is neuron#133," >&2
+    echo "which once hid five merged fixes including a P0 safety fix." >&2
+    echo "" >&2
+    echo "Sources that changed since the amalgam was generated:" >&2
+    diff <(printf '%s\n' "$RECORDED") <(printf '%s\n' "$CURRENT") \
+      | grep -E '^[<>]' | awk '{print "  " $1 " " $3}' | sort -u >&2
+    echo "" >&2
+    echo "Fix: regenerate the amalgam, then tools/soulc-stamp.sh --write" >&2
+    exit 1
+    ;;
+
+  *)
+    echo "usage: soulc-stamp.sh [--check|--write]" >&2; exit 2 ;;
+esac

vendor/el-runtime/v1.0.0-20260501/el_runtime.c

@@ -7175,6 +7175,12 @@ void engram_forget(el_val_t node_id) {
     if (idx < 0) return;
     /* Free node strings */
     EngramNode* n = &g->nodes[idx];
+    if (getenv("EG_DIAG")) {
+        fprintf(stderr, "[EG_DIAG] FORGET id=%s type=%s layer=%u label=%s\n",
+                sid, n->node_type ? n->node_type : "?", n->layer_id,
+                n->label ? n->label : "?");
+        fflush(stderr);
+    }
     free(n->id); free(n->content); free(n->node_type); free(n->label);
     free(n->tier); free(n->tags); free(n->metadata);
     free(n->emb);
@@ -7270,6 +7276,8 @@ el_val_t engram_prune_telemetry(el_val_t older_than_ms) {
         }
     }
     g->node_count = w;
+    if (getenv("EG_DIAG"))
+        fprintf(stderr, "[EG_DIAG] PRUNE_TELEMETRY removed=%lld\n", (long long)removed);
     if (removed == 0) { free(removed_ids); return 0; }
 
     /* Removed-id hash set (open addressing, power-of-two >= 2*removed). */
@@ -7327,6 +7335,39 @@ static int istr_contains(const char* hay, const char* needle) {
     return 0;
 }
 
+/* Word-START-anchored variant of istr_contains.
+ *
+ * WHY. The retrieval match primitive is a raw substring test, so a query token
+ * matches ANYWHERE inside a corpus word: "throom" matches "bathroom", "cat"
+ * matches "concatenate". Measured on this corpus over the 38-query gold set,
+ * that is not a rare accident — it is the bulk of some queries' candidate
+ * sets. q28's lexical leg is 36,954 records of which only 13 contain a query
+ * token at a word start (99.96% mid-word noise); six other queries carry
+ * ~20,500 mid-word-only records each; and the nonsense control q35
+ * ("xxqzzt vurblenacht throom") returns 7 records ALL of which match only
+ * mid-word, which is the entire reason that control has been dirty since main.
+ *
+ * WHAT CHANGES. A token must begin at a word boundary — the preceding
+ * character is not alphanumeric. Suffixes are still matched ("value" still
+ * hits "values", "unjailbreakable" still hits "unjailbreakables"), so this is
+ * strictly a prefix anchor, not whole-word equality; whole-word equality would
+ * break the morphological matching the phrase category depends on.
+ *
+ * PROVENANCE, stated honestly: this restores no engram claim. Will's design
+ * has no lexical leg at all (05-detailed-description l.64 takes "one or more
+ * seed node UUIDs representing the current active context" as its input), so
+ * the lexical leg is the seed-finding step that feeds the designed mechanism.
+ * Cleaner seeds serve that mechanism; they do not replace it. */
+static int istr_contains_wordstart(const char* hay, const char* needle) {
+    if (!hay || !needle || !*needle) return 0;
+    size_t nl = strlen(needle);
+    for (const char* p = hay; *p; p++) {
+        if (p != hay && isalnum((unsigned char)p[-1])) continue;
+        if (strncasecmp(p, needle, nl) == 0) return 1;
+    }
+    return 0;
+}
+
 /* ── Tokenized query matching ───────────────────────────────────────────
  * The engram query surface (search / activate / goal-bias) historically
  * matched the ENTIRE raw query string as a single case-insensitive
@@ -7379,9 +7420,9 @@ static int engram_node_match_score(const EngramNode* n,
                                    char toks[][ENGRAM_QTOK_LEN], int ntok) {
     int score = 0;
     for (int t = 0; t < ntok; t++) {
-        if (istr_contains(n->content, toks[t]) ||
-            istr_contains(n->label,   toks[t]) ||
-            istr_contains(n->tags,    toks[t]))
+        if (istr_contains_wordstart(n->content, toks[t]) ||
+            istr_contains_wordstart(n->label,   toks[t]) ||
+            istr_contains_wordstart(n->tags,    toks[t]))
             score++;
     }
     return score;
@@ -7396,9 +7437,9 @@ static uint32_t engram_node_match_mask(const EngramNode* n,
                                        char toks[][ENGRAM_QTOK_LEN], int ntok) {
     uint32_t m = 0;
     for (int t = 0; t < ntok && t < 32; t++) {
-        if (istr_contains(n->content, toks[t]) ||
-            istr_contains(n->label,   toks[t]) ||
-            istr_contains(n->tags,    toks[t]))
+        if (istr_contains_wordstart(n->content, toks[t]) ||
+            istr_contains_wordstart(n->label,   toks[t]) ||
+            istr_contains_wordstart(n->tags,    toks[t]))
             m |= (uint32_t)1u << t;
     }
     return m;
@@ -9271,6 +9312,26 @@ el_val_t engram_load(el_val_t path) {
         }
     }
     g->adj_dirty = 1;
+    if (getenv("EG_DIAG")) {
+        int64_t we = 0, wrongdim = 0;
+        for (int64_t i = 0; i < g->node_count; i++) {
+            if (g->nodes[i].emb) { we++; if (g->nodes[i].emb_dim != 768) wrongdim++; }
+        }
+        fprintf(stderr, "[EG_DIAG] loaded nodes=%lld with_emb=%lld wrongdim=%lld\n",
+                (long long)g->node_count, (long long)we, (long long)wrongdim);
+        const char* probe = getenv("EG_DIAG_ID");
+        if (probe) {
+            for (int64_t i = 0; i < g->node_count; i++) {
+                if (g->nodes[i].id && strcmp(g->nodes[i].id, probe) == 0) {
+                    fprintf(stderr, "[EG_DIAG] probe id=%s idx=%lld emb=%p dim=%d layer=%u addr=%d\n",
+                            probe, (long long)i, (void*)g->nodes[i].emb,
+                            (int)g->nodes[i].emb_dim, g->nodes[i].layer_id,
+                            eg_node_addressable(&g->nodes[i]));
+                }
+            }
+        }
+        fflush(stderr);
+    }
     /* Walk edges array */
     const char* edges_p = json_find_key(data, "edges");
     if (edges_p) {
@@ -9591,7 +9652,33 @@ el_val_t engram_get_node_by_label(el_val_t label) {
     return el_wrap_str(el_strdup("{}"));
 }
 
-el_val_t engram_search_json(el_val_t query, el_val_t limit) {
+/* ── THE SEARCH / RECALL BOUNDARY (2026-08-07) ───────────────────────────────
+ * engram_search_json is the LEXICAL function ~40 .el call sites already
+ * depend on: they pass a key-shaped string ("soul:boot_count",
+ * "soul-inbox-pending", a session label) and treat every returned record as
+ * a record that CONTAINS that key. Seven of those sites then delete what
+ * comes back (memory.el:176, sessions.el:250/268/444/523, soul.el:359 —
+ * "prune all existing X nodes, keep exactly one").
+ *
+ * The semantic and associative legs must therefore NOT live on this
+ * function. Claim 24 authorises the vector index "to respond to EMBEDDING
+ * SEARCH QUERIES by returning the node records whose embedding vectors have
+ * the highest cosine similarity to a query vector"; a keyed state read is
+ * not an embedding search query, it is the identifier-keyed retrieval of
+ * claim 23 ("node records are stored under a key encoding the node
+ * identifier"). Putting both behind one function erased that boundary, and
+ * a nearest neighbour of the string "soul:boot_count" is not a boot counter.
+ *
+ * MEASURED, on the harness corpus, isolated, read-only, no writes from any
+ * caller: 240 node records destroyed per boot, including 6 Knowledge nodes,
+ * a layer-1 "CORE IDENTITY — GENESIS, LINEAGE" Memory, and the value node
+ * `kn-58874a74` (gold answer for gold-set q15). The deletion list is the
+ * result list of the soul's own mem_boot_count_inc() lookup, in order.
+ *
+ * So: legs OFF here, legs ON in engram_recall_json below, which is what
+ * /api/neuron/recall reaches. Retrieval quality on the recall route is
+ * unchanged; the internal keyed reads get their contract back. */
+static el_val_t eg_search_json_impl(el_val_t query, el_val_t limit, int with_legs) {
     EngramStore* g = engram_get();
     const char* q = EL_CSTR(query);
     int64_t lim = (int64_t)limit;
@@ -9613,7 +9700,7 @@ el_val_t engram_search_json(el_val_t query, el_val_t limit) {
                  * so the semantic half of the retrieval surface has to land HERE
                  * to be observable to the MCP wrapper and the app. */
                 int32_t qdim = 0;
-                float*  qv   = eg_embed_fetch(q, &qdim);
+                float*  qv   = with_legs ? eg_embed_fetch(q, &qdim) : NULL;
                 EngramSemEntry* sem = qv ? malloc((size_t)g->node_count * sizeof(EngramSemEntry)) : NULL;
                 int64_t nsem = 0;
                 int64_t nhits = 0;
@@ -9654,12 +9741,28 @@ el_val_t engram_search_json(el_val_t query, el_val_t limit) {
                     }
                     if (sem && n->emb && n->emb_dim == qdim) {
                         double c = eg_cosine(n->emb, qv, qdim);
-                        /* Semantic leg: identical to eg_sem_term(), which is
-                         * left in place and still used by engram_search().
-                         * Inlined here only so one cosine serves both uses. */
-                        if (c > ENGRAM_EMBED_SEED_MIN) {
-                            double sv = (c - ENGRAM_EMBED_SEED_MIN) / (1.0 - ENGRAM_EMBED_SEED_MIN);
-                            if (sv > 1.0) sv = 1.0;
+                        /* Claim-24 semantic leg, restored verbatim: "returning
+                         * the node records whose embedding vectors have the
+                         * HIGHEST COSINE SIMILARITY to a query vector" — a
+                         * ranking, with no threshold anywhere in the claim.
+                         * ENGRAM_EMBED_SEED_MIN is defined at l.6094 as the
+                         * HippoRAG SEED-JOIN threshold; using it as a RESULT
+                         * filter here was never authorised, and it is a
+                         * per-query lottery rather than a quality gate: the
+                         * query's own top-1 cosine ranges 0.56-0.68 across the
+                         * held-out gold set, so 0.60 keeps a rank-1 answer for
+                         * one query and discards a rank-1 answer for the next.
+                         * Measured on the 30 held-out paraphrases: six golds
+                         * sit at global cosine rank 1-2 and score 0.564-0.589,
+                         * discarded by nothing but this constant.
+                         * What holds the nonsense controls is NOT this floor
+                         * but the corpus-vocabulary gate below (nhits == 0):
+                         * gibberish has no lexical seeds, so no leg reports.
+                         * Cosine is clamped to [0,1] per 05-detailed-description
+                         * l.69 ("clamped to [0,1] to prevent anti-correlated
+                         * embeddings from producing negative activation"). */
+                        double sv = c < 0.0 ? 0.0 : (c > 1.0 ? 1.0 : c);
+                        if (sv > 0.0) {
                             sem[nsem].idx = i; sem[nsem].sem = sv; nsem++;
                         }
                         /* Graph seeds: top-K by RAW cosine, insertion-ordered. */
@@ -9702,6 +9805,31 @@ el_val_t engram_search_json(el_val_t query, el_val_t limit) {
                 }
                 qsort(hits, (size_t)nhits, sizeof(EngramRankEntry), engram_rank_w_cmp);
                 if (sem) qsort(sem, (size_t)nsem, sizeof(EngramSemEntry), engram_sem_cmp);
+                if (getenv("EG_DIAG")) {
+                    int64_t we = 0, unaddr = 0, found = 0;
+                    const char* pid = getenv("EG_DIAG_ID");
+                    for (int64_t i = 0; i < g->node_count; i++) {
+                        if (g->nodes[i].emb) we++;
+                        if (!eg_node_addressable(&g->nodes[i])) unaddr++;
+                        if (pid && g->nodes[i].id && strcmp(g->nodes[i].id, pid) == 0) found++;
+                    }
+                    fprintf(stderr, "[EG_DIAG] STORE node_count=%lld with_emb=%lld unaddressable=%lld probe_found=%lld\n",
+                            (long long)g->node_count, (long long)we, (long long)unaddr, (long long)found);
+                    fprintf(stderr, "[EG_DIAG] q=\"%s\" qdim=%d nhits=%lld nsem=%lld\n",
+                            q, (int)qdim, (long long)nhits, (long long)nsem);
+                    for (int64_t k = 0; k < 5 && k < nsem; k++)
+                        fprintf(stderr, "[EG_DIAG]   sem[%lld] cos=%.4f id=%s\n",
+                                (long long)k, sem[k].sem, g->nodes[sem[k].idx].id);
+                    const char* probe = getenv("EG_DIAG_ID");
+                    if (probe) for (int64_t k = 0; k < nsem; k++)
+                        if (g->nodes[sem[k].idx].id
+                            && strcmp(g->nodes[sem[k].idx].id, probe) == 0) {
+                            fprintf(stderr, "[EG_DIAG]   probe at sem rank %lld cos=%.4f\n",
+                                    (long long)k, sem[k].sem);
+                            break;
+                        }
+                    fflush(stderr);
+                }
                 /* Claim-10 associative leg: expand the top lexical hits along
                  * structural relations only, order the reached set by query
                  * similarity. Empty whenever the seeds have no structural
@@ -9712,7 +9840,19 @@ el_val_t engram_search_json(el_val_t query, el_val_t limit) {
                     ? engram_assoc_leg(g, hits, nhits, semseed, nsemseed,
                                        qv, qdim, assoc, ENGRAM_ASSOC_MAX)
                     : 0;
-                int64_t* order = malloc((size_t)lim * sizeof(int64_t));
+                /* Corpus-vocabulary gate. If no stored record contains ANY
+                 * query token in its content, label or tags, the query is
+                 * outside this graph's vocabulary: there are no seeds, and
+                 * 05-detailed-description l.64 makes retrieval downstream of
+                 * seeds ("the caller provides one or more seed node UUIDs
+                 * representing the current active context"). No seeds, no
+                 * retrieval — the graph declines rather than confabulating a
+                 * nearest neighbour for gibberish. The mechanism is iteration
+                 * 6's (feat/claim24-unfloored-semantic); it is required here
+                 * because word-start matching empties the lexical leg for
+                 * q35-style queries whose only "hits" were mid-word, and the
+                 * semantic leg would otherwise answer them anyway. */
+                int64_t* order = (nhits > 0) ? malloc((size_t)lim * sizeof(int64_t)) : NULL;
                 if (order) {
                     int64_t no = engram_interleave3(hits, nhits, sem, nsem,
                                                     assoc, nassoc, lim, order);
@@ -9734,6 +9874,19 @@ el_val_t engram_search_json(el_val_t query, el_val_t limit) {
     return el_wrap_str(b.buf);
 }
 
+/* Lexical keyed read — the historical contract every internal caller relies
+ * on. Every returned record CONTAINS a query token. */
+el_val_t engram_search_json(el_val_t query, el_val_t limit) {
+    return eg_search_json_impl(query, limit, 0);
+}
+
+/* The retrieval surface: lexical + claim-24 semantic + claim-10 associative,
+ * rank-fused. Reached from handle_api_recall (/api/neuron/recall) — the route
+ * the MCP wrapper and the app call, and the one the eval harness measures. */
+el_val_t engram_recall_json(el_val_t query, el_val_t limit) {
+    return eg_search_json_impl(query, limit, 1);
+}
+
 el_val_t engram_scan_nodes_json(el_val_t limit, el_val_t offset) {
     EngramStore* g = engram_get();
     int64_t lim = (int64_t)limit; if (lim <= 0) lim = 100;

vendor/el-runtime/v1.0.0-20260501/el_runtime.h

@@ -612,6 +612,7 @@ el_val_t  engram_load(el_val_t path);
 el_val_t  engram_get_node_json(el_val_t id);
 el_val_t  engram_get_node_by_label(el_val_t label);
 el_val_t  engram_search_json(el_val_t query, el_val_t limit);
+el_val_t  engram_recall_json(el_val_t query, el_val_t limit);
 el_val_t  engram_scan_nodes_json(el_val_t limit, el_val_t offset);
 el_val_t  engram_scan_nodes_by_type_json(el_val_t node_type, el_val_t limit, el_val_t offset);
 el_val_t  engram_neighbors_json(el_val_t node_id, el_val_t max_depth, el_val_t direction);