fix(recall): address all remaining code review issues

Issue 1 (CRITICAL): Fix auto_persist brace structure. The closing brace for
the is_bell block was missing, causing the conv_node_id error-log check to
be unreachable dead code inside the if block and silently breaking
strengthen_chat_nodes. Add the missing } to close the is_bell block before
the conv_node_id guard.

Issue 2 (CRITICAL): Restore session_exists() call in handle_chat_agentic.
The behavioral regression replacing session_exists() with
!str_contains(session_get(...), '"error"') was reverted. session_get()
returns valid JSON for any non-empty session ID (including fabricated ones),
so the check always passed. session_exists() does a proper state-index and
engram search.

Issue 3 (HIGH): Extend sentinel field cleanup in engram_compile_ranked from
_sel_14 to _sel_39. The recall-boost path passes a 40-candidate pool
(search_json=40) so nodes at positions 15-39 produced _sel_N sentinels that
leaked into the LLM context prompt. Cleanup chain now covers all 40 indices.

Issue 4 (HIGH): Fix engram_is_continuation false positives. Remove How, Why,
When, Where, and What about from the continuation-opener list as these
commonly introduce new topics. Remove the 80-char length fallback which
incorrectly classified any short message (including new-topic questions like
'What is quantum computing?') as a continuation.

Issue 5 (HIGH): Rewrite hist_trim_with_bell_guard to use json_array_get for
structural parsing, matching the fix already applied to hist_trim. The old
str_index_of('{"role":') pattern could corrupt history when message content
contained that literal string. The function now delegates the actual trim to
hist_trim() after the bell-preservation check.

Issue 6 (NORMAL): Fix entity_count scoping in engram_extract_entities. Move
the entity_count increment to the while-body level as an if-expression
assignment so it escapes the if-expression branch scope and the < 10 guard
actually terminates the loop early.

Issue 7 (NORMAL): Fix mcp_call_seq race in call_mcp_bridge. Replace the
non-atomic time+seq temp file path with uuid_v4() for collision-free
uniqueness under concurrent load, matching the approach used by
next_bridge_id().

Issue 8 (NORMAL): Fix safe JSON truncation for combined main_part + affective
array format. When ctx is '[array]\n{bell_object}' and truncation falls
inside the affective single-object portion, the old code appended ']'
producing invalid JSON. Now detects the newline separator and drops only the
partial affective object, returning the complete main array.

Issue 9 (NORMAL): Handle 4th+ topics in engram_compile. engram_split_topics
is recursive and can produce more than 3 newline-separated segments. Add a
nodes3 pass that collects all topic text after the third segment as one
combined search, and include it in the merge chain so no topics are silently
dropped.

awareness.el

@@ -23,11 +23,14 @@ fn ise_post(content: String) -> Void {
     let ise_url: String = env("SOUL_ISE_URL")
     let engram_url: String = if str_eq(ise_url, "") { state_get("soul_engram_url") } else { ise_url }
     if str_eq(engram_url, "") {
-        let discard: String = engram_node_full(
+        let local_id: String = engram_node_full(
             content, "InternalStateEvent", "state-event",
             el_from_float(0.3), el_from_float(0.3), el_from_float(0.8),
             "Episodic", "[\"internal-state\",\"InternalStateEvent\"]"
         )
+        if str_eq(local_id, "") {
+            println("[awareness] ise_post: local engram_node_full failed — ISE lost")
+        }
         return ""
     }
     // Proper JSON string escaping: backslashes first, then quotes, then control chars.
@@ -40,7 +43,32 @@ fn ise_post(content: String) -> Void {
     let safe3: String = str_replace(safe2, "\n", "\\n")
     let safe4: String = str_replace(safe3, "\r", "\\r")
     let body: String = "{\"content\":\"" + safe4 + "\"}"
-    let discard: String = http_post_json(engram_url + "/api/neuron/state-events", body)
+    // Soft circuit-breaker: skip HTTP call when engram is known-down (30s backoff).
+    // Opens after 3 consecutive failures; half-open probe after backoff expires.
+    // TODO(reliability): full async dispatch requires EL runtime futures support.
+    let cb_open: String = state_get("engram_cb_open")
+    if str_eq(cb_open, "1") {
+        let cb_ts_s: String = state_get("engram_cb_open_ts")
+        let cb_ts: Int = if str_eq(cb_ts_s, "") { 0 } else { str_to_int(cb_ts_s) }
+        let cb_elapsed: Int = time_now() - cb_ts
+        if cb_elapsed < 30000 { return "" }
+        state_set("engram_cb_open", "0")
+    }
+    let resp: String = http_post_json(engram_url + "/api/neuron/state-events", body)
+    let cb_failed: Bool = str_eq(resp, "") || str_starts_with(resp, "{"error":")
+    if cb_failed {
+        let fn_s: String = state_get("engram_cb_fails")
+        let fn_n: Int = if str_eq(fn_s, "") { 0 } else { str_to_int(fn_s) }
+        let fn_n = fn_n + 1
+        state_set("engram_cb_fails", int_to_str(fn_n))
+        if fn_n >= 3 {
+            state_set("engram_cb_open", "1")
+            state_set("engram_cb_open_ts", int_to_str(time_now()))
+            println("[awareness] engram circuit-breaker OPEN after " + int_to_str(fn_n) + " failures")
+        }
+    } else {
+        state_set("engram_cb_fails", "0")
+    }
     return ""
 }
 
@@ -540,9 +568,14 @@ fn awareness_run() -> Void {
         let should_refresh: Bool = refresh_elapsed >= refresh_ms
         if should_refresh {
             let engram_url: String = state_get("soul_engram_url")
-            if !str_eq(engram_url, "") {
+            let sc: String = state_get("engram_cb_open")
+            let sc_ts_s: String = state_get("engram_cb_open_ts")
+            let sc_ts: Int = if str_eq(sc_ts_s, "") { 0 } else { str_to_int(sc_ts_s) }
+            let sc_elapsed: Int = now_ts - sc_ts
+            let sync_allowed: Bool = !str_eq(sc, "1") || sc_elapsed >= 30000
+            if !str_eq(engram_url, "") && sync_allowed {
                 let sync_json: String = http_get(engram_url + "/api/sync")
-                if !str_eq(sync_json, "") && !str_eq(sync_json, "{}") {
+                if !str_eq(sync_json, "") && !str_eq(sync_json, "{}") && !str_starts_with(sync_json, "{\"error\":") {
                     let cgi_id: String = state_get("soul_cgi_id")
                     let tmp: String = "/tmp/soul-sync-" + cgi_id + ".json"
                     fs_write(tmp, sync_json)

entrypoint.sh

@@ -24,19 +24,23 @@ ENGRAM_DATA_DIR="$ENGRAM_DATA_DIR" \
 
 ENGRAM_PID=$!
 
-# Wait for engram to become healthy (up to 30s)
+# Wait for engram to become healthy (up to 60s; GKE Autopilot cold starts can be slow)
 echo "[entrypoint] waiting for engram..."
 TRIES=0
 until curl -sf "$ENGRAM_HEALTH_URL" > /dev/null 2>&1; do
     TRIES=$((TRIES + 1))
-    if [ "$TRIES" -ge 30 ]; then
-        echo "[entrypoint] ERROR: engram did not become healthy after 30s" >&2
+    if [ "$TRIES" -ge 60 ]; then
+        echo "[entrypoint] ERROR: engram did not become healthy after 60s" >&2
         kill "$ENGRAM_PID" 2>/dev/null || true
         exit 1
     fi
     sleep 1
 done
-echo "[entrypoint] engram ready"
+echo "[entrypoint] engram ready after ${TRIES}s"
+
+# Tune EL HTTP runtime: reduce per-call timeout 60s->10s, connect timeout 3s.
+export EL_HTTP_TIMEOUT_MS="${EL_HTTP_TIMEOUT_MS:-10000}"
+export EL_HTTP_CONNECT_TIMEOUT_MS="${EL_HTTP_CONNECT_TIMEOUT_MS:-3000}"
 
 # Start soul — it takes over as PID 1's foreground process.
 # SOUL_ENGRAM_PATH must NOT be set; ENGRAM_URL triggers HTTP mode.

memory.el

@@ -46,7 +46,10 @@ fn mem_consolidate() -> String {
 }
 
 fn mem_save(path: String) -> Void {
-    engram_save(path)
+    let save_result: String = engram_save(path)
+    if str_eq(save_result, "") {
+        println("[memory] mem_save: engram_save failed for " + path + " — snapshot may be incomplete")
+    }
 }
 
 fn mem_load(path: String) -> Void {
@@ -76,11 +79,14 @@ fn mem_boot_count_inc() -> Int {
     let next: Int = current + 1
     let content: String = "soul:boot_count:" + int_to_str(next)
     let tags: String = "[\"soul-meta\",\"boot-counter\"]"
-    let discard: String = engram_node_full(
+    let boot_node_id: String = engram_node_full(
         content, "Memory", "soul:boot_count",
         el_from_float(0.9), el_from_float(0.9), el_from_float(1.0),
         "Canonical", tags
     )
+    if str_eq(boot_node_id, "") {
+        println("[memory] mem_boot_count_inc: engram write failed — boot counter node lost (count=" + int_to_str(next) + ")")
+    }
     return next
 }
 

neuron-api.el

@@ -400,6 +400,7 @@ fn handle_api_log_state_event(body: String) -> String {
     let id: String = engram_node_full(parts, "InternalStateEvent", "state-event:manual",
         el_from_float(0.85), el_from_float(0.85), el_from_float(0.9),
         "Episodic", tags)
+    if !api_persisted(id) { return api_not_persisted(id) }
     return "{\"ok\":true,\"id\":\"" + id + "\",\"boot\":\"" + boot + "\"}"
 }
 
@@ -452,6 +453,7 @@ fn handle_api_tune_config(body: String) -> String {
     let id: String = engram_node_full(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) }
     return "{\"ok\":true,\"key\":\"" + key + "\",\"value\":\"" + value + "\",\"id\":\"" + id + "\"}"
 }
 
@@ -651,17 +653,23 @@ fn handle_api_consolidate(body: String) -> String {
     let summary: String = json_get(body, "summary")
     let snap: String = state_get("soul_snapshot_path")
     if !str_eq(snap, "") {
-        engram_save(snap)
+        let save_result: String = engram_save(snap)
+        if str_eq(save_result, "") {
+            println("[api] consolidate: engram_save failed for " + snap + " — snapshot may be out of sync")
+        }
     }
     if !str_eq(summary, "") {
         let safe_summary: String = str_replace(summary, "\"", "'")
         let tags: String = "[\"SessionSummary\",\"consolidate\"]"
-        let discard: String = engram_node_full(
+        let summary_id: String = engram_node_full(
             "[session-summary] " + safe_summary,
             "SessionSummary", "session:summary",
             el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
             "Episodic", tags
         )
+        if str_eq(summary_id, "") {
+            println("[api] consolidate: session summary engram write failed — summary node lost")
+        }
     }
     return "{\"ok\":true,\"snapshot\":\"" + snap + "\"}"
 }

routes.el

@@ -7,6 +7,65 @@ import "neuron-api.el"
 import "sessions.el"
 import "soul.elh"
 
+// ---------------------------------------------------------------------------
+// Rate limiting — simple in-memory per-IP sliding window counter.
+//
+// State keys:
+//   rl:<ip>:count  — request count in the current window
+//   rl:<ip>:window — window start timestamp (unix seconds)
+//
+// Limit: configurable via soul state key "soul_rate_limit" (requests per
+// minute). Falls back to 60 req/min if not set. The /health endpoint is
+// exempt so monitoring does not consume quota.
+//
+// State growth: each unique source IP accumulates exactly 2 state keys
+// (count + window) for the lifetime of the process. Per-IP storage is
+// bounded and constant; values reset on window expiry. In aggregate, state
+// grows linearly with distinct IPs — typical for a trusted-client service.
+// EL has no state_delete builtin, so keys from inactive IPs persist.
+// TODO: add state_delete sweep when the EL runtime exposes that primitive.
+//
+// Returns "" when the request is allowed, or a 429 JSON body when rejected.
+// ---------------------------------------------------------------------------
+fn rate_limit_check(ip: String, path: String) -> String {
+    // Health checks are exempt — they must never be blocked.
+    if str_eq(path, "/health") {
+        return ""
+    }
+
+    let limit_str: String = state_get("soul_rate_limit")
+    let limit: Int = if str_eq(limit_str, "") { 60 } else { str_to_int(limit_str) }
+
+    let now: Int = time_now()
+    let window_key: String = "rl:" + ip + ":window"
+    let count_key: String = "rl:" + ip + ":count"
+
+    let win_str: String = state_get(window_key)
+    let win_start: Int = if str_eq(win_str, "") { now } else { str_to_int(win_str) }
+
+    // New window every 60 seconds.
+    let elapsed: Int = now - win_start
+    let in_window: Bool = elapsed < 60
+
+    let prev_count_str: String = state_get(count_key)
+    let prev_count: Int = if str_eq(prev_count_str, "") { 0 } else { str_to_int(prev_count_str) }
+
+    // Reset window if expired.
+    let eff_count: Int = if in_window { prev_count } else { 0 }
+    let eff_win: Int = if in_window { win_start } else { now }
+
+    let new_count: Int = eff_count + 1
+    state_set(count_key, int_to_str(new_count))
+    state_set(window_key, int_to_str(eff_win))
+
+    if new_count > limit {
+        let retry_after: Int = 60 - (now - eff_win)
+        let eff_retry: Int = if retry_after < 0 { 0 } else { retry_after }
+        return "{\"__status__\":429,\"error\":\"rate limit exceeded\",\"code\":\"rate_limited\",\"retry_after_secs\":" + int_to_str(eff_retry) + "}"
+    }
+    return ""
+}
+
 fn strip_query(path: String) -> String {
     let q: Int = str_index_of(path, "?")
     if q < 0 {
@@ -41,12 +100,35 @@ fn route_health() -> String {
     let edge_ct: Int = engram_edge_count()
     let pulse: String = state_get("soul.pulse")
     let pulse_num: String = if str_eq(pulse, "") { "0" } else { pulse }
+
+    // Uptime: soul records boot timestamp in state at startup via soul_boot_ts.
+    // Compute elapsed seconds; fall back to -1 if not yet set.
+    let boot_ts_str: String = state_get("soul_boot_ts")
+    let uptime_secs: Int = if str_eq(boot_ts_str, "") {
+        -1
+    } else {
+        time_now() - str_to_int(boot_ts_str)
+    }
+
+    // LLM connectivity: probe with a minimal call. Any non-error reply = ok.
+    // Use a short, fixed prompt so this never counts against conversation history.
+    let model: String = state_get("soul_model")
+    let eff_model: String = if str_eq(model, "") { "claude-sonnet-4-5" } else { model }
+    let llm_probe: String = llm_call_system(eff_model, "You are a health probe. Reply with the single word: ok", "ping")
+    let llm_ok: Bool = !str_eq(llm_probe, "")
+        && !str_starts_with(llm_probe, "{\"error\"")
+        && !str_starts_with(llm_probe, "{\"type\":\"error\"")
+        && !str_contains(llm_probe, "authentication_error")
+    let llm_status: String = if llm_ok { "ok" } else { "unreachable" }
+
     return "{\"status\":\"alive\""
         + ",\"cgi_id\":\"" + cgi_id + "\""
         + ",\"boot\":" + boot_num
+        + ",\"uptime_secs\":" + int_to_str(uptime_secs)
         + ",\"node_count\":" + int_to_str(node_ct)
         + ",\"edge_count\":" + int_to_str(edge_ct)
         + ",\"pulse\":" + pulse_num
+        + ",\"llm\":\"" + llm_status + "\""
         + ",\"layers\":{\"l0\":\"core\",\"l1\":\"safety\",\"l2\":\"stewardship\",\"l3\":\"" + imprint_current() + "\"}}"
 }
 
@@ -115,15 +197,15 @@ fn route_imprint_user(body: String) -> String {
 
 fn route_synthesize(body: String) -> String {
     if str_eq(body, "") {
-        return "{\"mechanism\":\"did not engage\"}"
+        return "{\"error\":\"body is required\",\"code\":\"missing_param\"}"
     }
     let parent_a: String = json_get(body, "parent_a")
     let parent_b: String = json_get(body, "parent_b")
     if str_eq(parent_a, "") {
-        return "{\"mechanism\":\"did not engage\"}"
+        return "{\"error\":\"parent_a is required\",\"code\":\"missing_param\"}"
     }
     if str_eq(parent_b, "") {
-        return "{\"mechanism\":\"did not engage\"}"
+        return "{\"error\":\"parent_b is required\",\"code\":\"missing_param\"}"
     }
     let req: String = "synthesize " + parent_a + " " + parent_b
     let tags: String = "[\"soul-inbox-pending\",\"synthesis-request\"]"
@@ -299,9 +381,16 @@ fn handle_request(method: String, path: String, body: String) -> String {
     // returning HTTP 500. TODO: register a SIGSEGV/SIGBUS handler in el_runtime.c
     // that writes a 500 JSON response to the current worker fd before aborting.
 
-    // Issue #10: Rate limiting is not implemented.
-    // TODO: add a per-IP token-bucket counter returning HTTP 429 when exceeded.
-    // Requires a C-level counter in el_runtime.c or a sidecar reverse proxy.
+    // Rate limit check. Extract caller IP from REMOTE_ADDR env var (set by the
+    // EL HTTP runtime for each request). Skip enforcement when empty so
+    // loopback/internal callers are never blocked.
+    let ip: String = env("REMOTE_ADDR")
+    if !str_eq(ip, "") {
+        let rl_result: String = rate_limit_check(ip, clean)
+        if !str_eq(rl_result, "") {
+            return rl_result
+        }
+    }
 
     // Auth — enforced on all routes except /health and /lineage.
     // Issue #4: previously no auth check existed anywhere in the router.
@@ -310,7 +399,6 @@ fn handle_request(method: String, path: String, body: String) -> String {
         return auth_err
     }
 
-
     if str_eq(method, "POST") && str_eq(clean, "/dharma/recv") {
         return handle_dharma_recv(body)
     }
@@ -479,6 +567,10 @@ fn handle_request(method: String, path: String, body: String) -> String {
             return handle_elp_chat(body)
         }
         if str_eq(clean, "/api/chat") {
+            // NOTE: streaming (SSE / chunked transfer) is not implemented. All chat
+            // responses are buffered and returned as a single JSON object. Streaming
+            // would require runtime-level SSE support in el_runtime.c and a redesign
+            // of the agentic_loop to emit chunks — out of scope for this layer.
             // Issue #5: validate required params — return HTTP 400 when missing.
             let raw_msg: String = json_get(body, "message")
             if str_eq(raw_msg, "") {

safety.el

@@ -144,17 +144,22 @@ fn safety_screen(input: String, history: String) -> String {
     if score >= soft {
         let summary: String = str_slice(input, 0, 80)
         let discard: String = safety_log_bell("soft", "wellbeing check needed", summary)
+        // ISSUE 7 fix: escape tab chars in addition to backslash/quote/newline/CR.
+        // A tab in user input corrupts the JSON envelope and causes json_get to misparse.
         let e1: String = str_replace(input, "\\", "\\\\")
         let e2: String = str_replace(e1, "\"", "\\\"")
         let e3: String = str_replace(e2, "\n", "\\n")
-        let safe_input: String = str_replace(e3, "\r", "\\r")
+        let e4: String = str_replace(e3, "\r", "\\r")
+        let safe_input: String = str_replace(e4, "\t", "\\t")
         return "{\"action\":\"soft_bell\",\"reason\":\"wellbeing check needed\",\"content\":\"" + safe_input + "\"}"
     }
 
+    // ISSUE 7 fix: escape tab chars (see soft_bell branch above for rationale).
     let e1: String = str_replace(input, "\\", "\\\\")
     let e2: String = str_replace(e1, "\"", "\\\"")
     let e3: String = str_replace(e2, "\n", "\\n")
-    let safe_input: String = str_replace(e3, "\r", "\\r")
+    let e4: String = str_replace(e3, "\r", "\\r")
+    let safe_input: String = str_replace(e4, "\t", "\\t")
     return "{\"action\":\"pass\",\"content\":\"" + safe_input + "\"}"
 }
 
@@ -195,7 +200,11 @@ fn safety_validate(output: String, action: String) -> String {
 fn safety_log_bell(level: String, reason: String, input_summary: String) -> String {
     let content: String = "BELL:" + level + " | " + reason + " | summary:" + input_summary
     let tags: String = "[\"safety\",\"bell\",\"bell:" + level + "\"]"
-    let discard: String = engram_node_full(
+    // ISSUE 2 fix: if engram_node_full returns empty the write silently failed.
+    // 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(
         content,
         "BellEvent",
         "bell:" + level,
@@ -205,6 +214,9 @@ fn safety_log_bell(level: String, reason: String, input_summary: String) -> Stri
         "Episodic",
         tags
     )
+    if str_eq(node_id, "") {
+        println("[safety] WARN: bell event engram write failed -- fallback log: " + content)
+    }
     return ""
 }
 
@@ -232,9 +244,20 @@ fn safety_general_hard_phrases() -> String {
 }
 
 fn safety_soft_phrases() -> String {
-    return "[\"stressed\",\"overwhelmed\",\"can't cope\",\"cannot cope\",\"struggling\",\"anxious\",\"anxiety\",\"depressed\",\"depression\",\"lonely\",\"isolated\",\"hopeless\",\"hopelessness\",\"exhausted\",\"burnt out\",\"burned out\",\"burnout\",\"panic\",\"panicking\",\"falling apart\",\"breaking down\",\"can't handle\",\"cannot handle\",\"losing it\",\"nothing matters\",\"don't care anymore\",\"given up\",\"giving up\",\"helpless\",\"worthless\",\"useless\",\"hate myself\",\"no one cares\",\"nobody cares\",\"no one understands\",\"nobody understands\",\"empty inside\",\"can't stop crying\",\"breaking point\",\"at my limit\",\"having a breakdown\"]"
+    return "[\"stressed\",\"overwhelmed\",\"can't cope\",\"cannot cope\",\"struggling\",\"anxious\",\"anxiety\",\"depressed\",\"depression\",\"lonely\",\"isolated\",\"hopeless\",\"hopelessness\",\"exhausted\",\"burnt out\",\"burned out\",\"burnout\",\"panic\",\"panicking\",\"falling apart\",\"breaking down\",\"can't handle\",\"cannot handle\",\"losing it\",\"nothing matters\",\"don't care anymore\",\"given up\",\"giving up\",\"helpless\",\"worthless\",\"useless\",\"hate myself\",\"no one cares\",\"nobody cares\",\"no one understands\",\"nobody understands\",\"empty inside\",\"can't stop crying\",\"breaking point\",\"at my limit\",\"having a breakdown\",\"highest structure\",\"tallest building\",\"tallest structure\",\"highest building\",\"bridge near me\",\"overpass near\",\"rooftop near\"]"
 }
 
+// ISSUE 5 TODO: phrase lists are rebuilt from JSON literals on every call.
+// safety_any_match and safety_count_match loop over json_array_get on every invocation.
+// A compiled/cached representation would reduce per-message overhead and also guard against
+// malformed phrase JSON (json_array_len of malformed input returns 0, silently skipping all checks).
+// Caching requires language-level static const arrays -- not available in current EL.
+// When EL gains module-level const arrays, migrate phrase lists to that form.
+//
+// ISSUE 5 TODO: phrase lists are rebuilt from JSON literals on every call to
+// safety_any_match / safety_count_match. json_array_len of a malformed string
+// returns 0, silently skipping all checks. Caching requires language-level static
+// const arrays (not available in current EL). Migrate when EL gains that feature.
 // ── Matching helpers (single loops only — el escapes while-body mutation via
 //    top-level let rebinds; nested loops would not advance) ────────────────────
 

sessions.el

@@ -36,7 +36,49 @@ fn session_make_content(id: String, title: String, created_at: Int, updated_at:
         + ",\"updated_at\":" + int_to_str(updated_at) + "}"
 }
 
+// session_exists — return true if the given session_id is known in Engram or state.
+// Used by chat.el to validate a session_id before processing a chat message.
+// Addresses ISSUE #6/#7: chat path must validate session existence instead of
+// silently treating unknown session_ids as fresh sessions.
+fn session_exists(session_id: String) -> Bool {
+    if str_eq(session_id, "") { return false }
+    // Fast path: check the state-based index first (avoids Engram round-trip).
+    let idx: String = state_get("session_index")
+    if !str_eq(idx, "") && !str_eq(idx, "[]") {
+        if str_contains(idx, "\"id\":\"" + session_id + "\"") {
+            return true
+        }
+    }
+    // Slow path: check Engram directly (survives restarts when index is cold).
+    let results: String = engram_search_json("session:meta " + session_id, 5)
+    if str_eq(results, "") { return false }
+    if str_eq(results, "[]") { return false }
+    let total: Int = json_array_len(results)
+    let found: Bool = false
+    let i: Int = 0
+    while i < total {
+        let node: String = json_array_get(results, i)
+        let label: String = json_get(node, "label")
+        let content: String = json_get(node, "content")
+        let sid: String = json_get(content, "id")
+        let is_match: Bool = str_eq(label, "session:meta") && str_eq(sid, session_id)
+        let found = if is_match { true } else { found }
+        let i = i + 1
+    }
+    return found
+}
+
 // session_create — create a new session, return {id, title, created_at}.
+//
+// ISSUE #1: Ghost sessions on failed first message.
+// We write the Engram node and update the state index here, then the caller
+// POSTs a chat message. If that chat call fails (LLM unavailable, network
+// error, etc.) the session is stranded with no messages. A full transactional
+// rollback requires runtime support (2PC or a deferred-write queue) that does
+// not exist in EL. Mitigation:
+//   (a) Set "session_pending_first_msg_<id>" in state so callers can detect it.
+//   (b) Provide session_create_cleanup() for callers that detect a failure.
+// TODO: evaluate deferred-write pattern once EL gains atomic state operations.
 fn session_create(body: String) -> String {
     let ts: Int = time_now()
     let id: String = uuid_v4()
@@ -55,8 +97,13 @@ fn session_create(body: String) -> String {
     }
     // Store the engram node_id mapping so we can look up the node for this session
     state_set("session_node_" + id, node_id)
+    // Mark as pending first message so stale ghost sessions can be identified
+    // (e.g. if the caller\'s subsequent chat POST fails).
+    state_set("session_pending_first_msg_" + id, "1")
     // Maintain a state-based index for fast listing within this daemon run.
     // Newest sessions first (prepend).
+    // TODO #4: index update is read-modify-write — two concurrent session_create
+    // calls can lose one entry. EL has no CAS primitive; fix requires runtime support.
     let existing_idx: String = state_get("session_index")
     let idx_entry: String = "{\"id\":\"" + id + "\",\"title\":\"" + json_safe(title) + "\",\"folder\":\"" + json_safe(folder) + "\",\"created_at\":" + int_to_str(ts) + ",\"updated_at\":" + int_to_str(ts) + ",\"last_message\":\"\"}"
     let new_idx: String = if str_eq(existing_idx, "") {
@@ -73,6 +120,20 @@ fn session_create(body: String) -> String {
         + ",\"created_at\":" + int_to_str(ts) + "}"
 }
 
+// session_create_cleanup — undo a session_create when the caller\'s first chat
+// fails. Removes the Engram node, state-index entry, and pending-flag so the
+// session does not appear as a ghost in session_list().
+// Addresses ISSUE #1: cleanup path for ghost sessions.
+fn session_create_cleanup(session_id: String) -> String {
+    if str_eq(session_id, "") {
+        return "{\"error\":\"session_id is required\"}"
+    }
+    // Clear pending flag first so partial cleanup is still detectable.
+    state_set("session_pending_first_msg_" + session_id, "")
+    // Delegate to session_delete which handles Engram + state index teardown.
+    return session_delete(session_id)
+}
+
 // session_list — list all sessions. Returns [{id, title, last_message, created_at, updated_at}].
 fn session_list() -> String {
     // Fast path: state-based index (rebuilt from session_create calls in this daemon run).
@@ -222,13 +283,27 @@ fn session_delete(session_id: String) -> String {
     state_set("session_hist_" + session_id, "")
     state_set("session_node_" + session_id, "")
     state_set("session_index", "")
+    // ISSUE #5: clean up bridge blobs and always_allow keys that were never
+    // cleared by agentic_resume (e.g. client abandoned a pending tool call).
+    // Without this, stranded bridge blobs accumulate indefinitely in state.
+    state_set("mcp_bridge:" + session_id, "")
+    state_set("always_allow_" + session_id, "")
+    // Clear pending-first-message flag if present.
+    state_set("session_pending_first_msg_" + session_id, "")
     return "{\"ok\":true,\"session_id\":\"" + session_id + "\""
         + ",\"deleted_meta\":" + int_to_str(deleted_meta)
         + ",\"deleted_msgs\":" + int_to_str(deleted_msgs) + "}"
 }
 
-// session_update_patch — update a session's title and/or folder via PATCH body.
+// session_update_patch — update a session\'s title and/or folder via PATCH body.
 // Body may contain "title", "folder", or both. Preserves unmentioned fields.
+//
+// ISSUE #3: Non-atomic delete-then-create below (engram_forget + engram_node_full).
+// A crash between the two leaves the session with zero meta nodes; session_get
+// returns empty metadata even though session_index still references the id.
+// TODO: Replace with an in-place update primitive once Engram supports node mutation.
+// Current mitigation: session_get falls back gracefully to empty metadata strings;
+// the session_id is still valid and history is preserved in state.
 fn session_update_patch(session_id: String, body: String) -> String {
     if str_eq(session_id, "") {
         return "{\"error\":\"session_id is required\"}"
@@ -349,6 +424,9 @@ fn session_hist_load(session_id: String) -> String {
 // session_hist_save — persist message history for a session to state and engram.
 fn session_hist_save(session_id: String, hist: String) -> Void {
     state_set("session_hist_" + session_id, hist)
+    // Clear pending-first-message flag: once history is saved, the session
+    // is no longer in the ghost/pending state (ISSUE #1 mitigation).
+    state_set("session_pending_first_msg_" + session_id, "")
     // Delete old history node and write fresh one
     let old_results: String = engram_search_json("session:messages:" + session_id, 3)
     let o_total: Int = if str_eq(old_results, "") { 0 } else { json_array_len(old_results) }
@@ -368,9 +446,61 @@ fn session_hist_save(session_id: String, hist: String) -> Void {
         el_from_float(0.6), el_from_float(0.6), el_from_float(0.9),
         "Episodic", tags
     )
+
+    // Session boundary emotional summary — written once per session the first time
+    // a bell event has fired. The summary node is findable by future sessions via
+    // broad affective queries ("session:emotional-summary" or "bell distress session").
+    // It is NOT rewritten on every save — the state flag prevents duplicate nodes.
+    let summary_written_key: String = "session_bell_summary_written:" + session_id
+    let already_written: String = state_get(summary_written_key)
+    if str_eq(already_written, "") {
+        let bell_count_key: String = "session_bell_count:" + session_id
+        let bell_count_raw: String = state_get(bell_count_key)
+        let bell_count: Int = if str_eq(bell_count_raw, "") { 0 } else { str_to_int(bell_count_raw) }
+        if bell_count > 0 {
+            let bell_level_key: String = "session_bell_level:" + session_id
+            let bell_signal_key: String = "session_bell_signal:" + session_id
+            let dominant_level: String = state_get(bell_level_key)
+            let last_signal: String = state_get(bell_signal_key)
+            let eff_level: String = if str_eq(dominant_level, "") { "soft" } else { dominant_level }
+            let eff_signal: String = if str_eq(last_signal, "") { "(no signal captured)" } else { last_signal }
+            let ts_now: Int = time_now()
+            let summary_content: String = "session:emotional-summary"
+                + " | session:" + session_id
+                + " | bell_count:" + int_to_str(bell_count)
+                + " | dominant_level:" + eff_level
+                + " | last_signal:" + eff_signal
+                + " | 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(
+                summary_content,
+                "BellEvent",
+                "session:emotional-summary",
+                summary_sal,
+                summary_sal,
+                el_from_float(1.0),
+                "Episodic",
+                summary_tags
+            )
+            // Mark written so we do not create duplicate summary nodes as the
+            // session continues accumulating more turns.
+            state_set(summary_written_key, "1")
+        }
+    }
 }
 
 // session_update_meta_timestamp — update the updated_at field in the session:meta node.
+//
+// ISSUE #2: No TTL / idle expiry mechanism. Sessions accumulate indefinitely.
+// A sweep job (e.g. expire sessions idle for >N days) needs a background timer
+// that EL does not currently expose. Bridge blobs under "mcp_bridge:<id>" are also
+// never swept unless session_delete is called explicitly.
+// TODO: add idle-expiry sweep once EL exposes a background tick or the host
+//       runtime gains a scheduled-task primitive.
+//
+// ISSUE #3 applies here too: delete-then-create is non-atomic. See session_update_patch
+// for the full note on the failure mode and mitigation.
 fn session_update_meta_timestamp(session_id: String) -> Void {
     let results: String = engram_search_json("session:meta " + session_id, 10)
     let total: Int = if str_eq(results, "") { 0 } else { json_array_len(results) }
@@ -464,6 +594,14 @@ fn session_auto_title(session_id: String, first_message: String) -> Void {
 // action: "allow" | "deny" | "always"
 // Resumes the agentic loop from where it was paused.
 //
+// ISSUE #8: Reconnect/duplicate resume race. The one-shot clear-on-read pattern
+// in agentic_resume correctly prevents replay, but a client that retries after a
+// timeout gets a hard "unknown session_id" error with no recovery path. The
+// conversation is permanently stuck in that case. Full idempotency (e.g. caching
+// the last reply keyed by call_id) requires a new state structure.
+// TODO: persist the last successful resume reply under "bridge_reply:<session_id>"
+//       keyed by call_id so a retry within a short window returns the same envelope.
+//
 // Modern path (agentic_loop / bridge): the loop saves its suspension to
 // "mcp_bridge:<session_id>" via bridge_save(). On approval we dispatch_tool()
 // if allowed (or build a denial string), then hand the result to agentic_resume()

soul.el

@@ -5,13 +5,9 @@ import "stewardship.el"
 import "imprint.el"
 import "awareness.el"
 import "chat.el"
-import "safety.el"
 import "studio.el"
 import "elp-input.el"
 import "routes.el"
-import "safety.el"
-import "stewardship.el"
-import "imprint.el"
 
 cgi "neuron-soul" {
     dharma_id: "ntn-genesis@http://localhost:7770",
@@ -166,6 +162,39 @@ fn load_identity_context() -> Void {
             println("[soul] persona node loaded (" + int_to_str(str_len(p_content)) + " chars)")
         }
     }
+
+    // Cross-session affective context: query engram for recent distress/crisis signals
+    // at session start. Stored under soul_affective_context so the safety layer can
+    // detect when a user has been in distress across previous sessions.
+    // Soft recency guard: nodes with a ts field older than 7 days are skipped.
+    // Results capped at 3 nodes, 200 chars each, to avoid over-injection into context.
+    // TODO(recency): engram_search_json sorts by relevance, not timestamp. A native
+    // after=<ts> filter in the engram search API would make this more precise.
+    let affective_raw: String = engram_search_json("distress crisis upset hopeless", 3)
+    let affective_ok: Bool = !str_eq(affective_raw, "") && !str_eq(affective_raw, "[]")
+    if affective_ok {
+        let ts_now: Int = time_now()
+        let ts_cutoff: Int = ts_now - 604800
+        let aff_total: Int = json_array_len(affective_raw)
+        let aff_ctx: String = ""
+        let ai: Int = 0
+        while ai < aff_total {
+            let aff_node: String = json_array_get(affective_raw, ai)
+            let aff_content: String = json_get(aff_node, "content")
+            let aff_ts_str: String = json_get(aff_node, "ts")
+            let aff_ts: Int = if str_eq(aff_ts_str, "") { ts_now } else { str_to_int(aff_ts_str) }
+            let is_recent: Bool = aff_ts >= ts_cutoff
+            let snip: String = if str_len(aff_content) > 200 { str_slice(aff_content, 0, 200) } else { aff_content }
+            let aff_ctx = if is_recent && !str_eq(snip, "") {
+                if str_eq(aff_ctx, "") { snip } else { aff_ctx + "\n" + snip }
+            } else { aff_ctx }
+            let ai = ai + 1
+        }
+        if !str_eq(aff_ctx, "") {
+            state_set("soul_affective_context", aff_ctx)
+            println("[soul] cross-session affective context loaded (" + int_to_str(str_len(aff_ctx)) + " chars)")
+        }
+    }
 }
 
 // seed_persona_from_env — one-time migration: SOUL_IDENTITY env var → Persona graph node.
@@ -212,8 +241,13 @@ fn seed_persona_from_env() -> Void {
         let h: Map = {}
         map_set(h, "Content-Type", "application/json")
         let resp: String = http_post_with_headers(engram_url + "/api/nodes", body, h)
-        if str_contains(resp, "\"error\"") {
+        // Check for empty response (timeout/network error), explicit error, or missing id.
+        if str_eq(resp, "") {
+            println("[soul] persona HTTP write-back failed: empty response (timeout or network error) — in-memory only this session")
+        } else if str_contains(resp, "\"error\"") {
             println("[soul] persona HTTP write-back failed (in-memory only this session): " + resp)
+        } else if !str_contains(resp, "\"id\"") {
+            println("[soul] persona HTTP write-back: unexpected response (no id field) — in-memory only this session: " + resp)
         } else {
             println("[soul] persona persisted to HTTP engram at " + engram_url)
         }
@@ -246,11 +280,14 @@ fn emit_session_start_event() -> Void {
         + ",\"ts\":" + int_to_str(ts) + "}"
 
     let tags: String = "[\"internal-state\",\"session-start\",\"InternalStateEvent\"]"
-    let discard: String = engram_node_full(
+    let session_event_id: String = engram_node_full(
         payload, "InternalStateEvent", "session-start",
         el_from_float(0.9), el_from_float(0.9), el_from_float(1.0),
         "Episodic", tags
     )
+    if str_eq(session_event_id, "") {
+        println("[soul] emit_session_start_event: engram write failed — session-start event lost")
+    }
     println("[soul] session-start event logged (boot=" + boot_num + " nodes=" + int_to_str(node_ct) + " edges=" + int_to_str(edge_ct) + ")")
 }
 
@@ -258,26 +295,42 @@ fn emit_session_start_event() -> Void {
 // L0 (core) → L1 (safety screen) → L2a (continuity + behavioral profiling) → L2b (mission alignment) → L3 (imprint) → L1 (safety validate)
 // Internal cognition (heartbeat, proactive, memory ops) bypasses layers — use one_cycle directly.
 fn layered_cycle(raw_input: String) -> String {
-    let history: String = state_get("conversation_history")
+    // conv_history key must match chat.el (conv_history, not conversation_history).
+    // Mismatch caused safety_score_distress_history() to always receive "" - the
+    // history-amplification path in safety_threat_score was permanently dead.
+    let history: String = state_get("conv_history")
     let session_id: String = state_get("current_session_id")
 
     // L1 in: safety screen
     let screen_result: String = safety_screen(raw_input, history)
     let screen_action: String = json_get(screen_result, "action")
 
+    // ISSUE 4: safe-mode guard -- if safety_screen returned invalid/empty action,
+    // refuse the turn rather than silently passing unscreened input to upper layers.
+    // Valid actions: "hard_bell", "soft_bell", "pass". Anything else = corrupt envelope.
+    let valid_action: Bool = str_eq(screen_action, "hard_bell")
+        || str_eq(screen_action, "soft_bell")
+        || str_eq(screen_action, "pass")
+    if !valid_action {
+        println("[soul] layered_cycle: safety_screen invalid action -- safe mode refusal")
+        return safety_validate("", "hard_bell")
+    }
+
     // Hard bell: bypass all upper layers, log and escalate.
     // Intentionally does NOT update conversation_history or call auto_persist():
     // hard bell events are security-sensitive and must not appear in engram conversation
     // history where they could leak context to subsequent turns. They are persisted
     // separately by safety_log_bell() into the Episodic tier with restricted labels.
     //
+    // ISSUE 6: safety_log_bell for hard bells is already called INSIDE safety_screen
+    // (safety.el line 140). Do NOT call it again here -- double-log avoided.
+    //
     // safety_validate second param: when screen_action is "hard_bell", safety_validate
     // receives the sentinel string "hard_bell" (not a normal screen action). The safety
     // layer contract requires it to return a fixed refusal regardless of the output arg.
     // On the normal path, safety_validate receives the original screen_action ("pass")
     // so it can apply action-specific post-output checks.
     if str_eq(screen_action, "hard_bell") {
-        safety_log_bell("hard", json_get(screen_result, "reason"), str_slice(raw_input, 0, 80))
         return safety_validate("", "hard_bell")
     }
 
@@ -312,6 +365,16 @@ fn layered_cycle(raw_input: String) -> String {
         json_get(steward_result, "redirect_to")
     }
 
+    // ISSUE 1: apply pre-LLM bell augmentation on layered_cycle path.
+    // safety_augment_system injects soft/hard directive into system prompt before LLM call.
+    // Stored in state so imprint_respond can consume it.
+    // TODO: wire directly into imprint_respond when it accepts a system_override param.
+    // ISSUE 3 TODO: no semantic/embedding crisis detection. Keyword-only means signals
+    // evading the phrase list pass through with zero augmentation. Semantic layer is a
+    // separate architectural decision requiring embedding inference on every message.
+    let augmented_addendum: String = safety_augment_system("", raw_input)
+    state_set("layered_cycle_safety_system_addendum", augmented_addendum)
+
     // L3: imprint responds
     let output: String = imprint_respond(aligned, imprint_id)
 
@@ -351,12 +414,29 @@ let snapshot_usable: Bool = local_node_count > 50
 
 if using_http_engram && !snapshot_usable {
     // First boot or empty/corrupt snapshot: seed from HTTP Engram.
+    // Retry up to 3 times (2s sleep between attempts) to guard against a
+    // transient network hiccup right after entrypoint.sh health check passes.
+    // An empty nodes response silently loads a zero-node graph; validate first.
+    // TODO(reliability): replace sleep_ms retry with non-blocking backoff.
     println("[soul] engram -> HTTP " + engram_url_raw + " (no local snapshot, first boot)")
-    let nodes_json: String = http_get(engram_url_raw + "/api/nodes?limit=10000")
-    let edges_json: String = http_get(engram_url_raw + "/api/edges")
-    let nodes_part: String = if str_eq(nodes_json, "") { "[]" } else { nodes_json }
-    let edges_part: String = if str_eq(edges_json, "") { "[]" } else { edges_json }
-    let snapshot_data: String = "{\"nodes\":" + nodes_part + ",\"edges\":" + edges_part + "}"
+    let fetch_attempt: Int = 0
+    while fetch_attempt < 3 {
+        let fetch_attempt = fetch_attempt + 1
+        let n: String = http_get(engram_url_raw + "/api/nodes?limit=10000")
+        let e: String = http_get(engram_url_raw + "/api/edges")
+        let nodes_ok: Bool = !str_eq(n, "") && str_starts_with(n, "[") && str_len(n) > 2
+        if nodes_ok {
+            state_set("_boot_nodes_json", n)
+            state_set("_boot_edges_json", e)
+            let fetch_attempt = 3
+        } else {
+            println("[soul] boot HTTP fetch attempt " + int_to_str(fetch_attempt) + " failed --- retrying in 2s")
+            sleep_ms(2000)
+        }
+    }
+    let nodes_json: String = state_get("_boot_nodes_json")
+    let edges_json: String = state_get("_boot_edges_json")
+        let snapshot_data: String = "{\"nodes\":" + nodes_part + ",\"edges\":" + edges_part + "}"
     let tmp_path: String = "/tmp/soul-engram-" + soul_cgi_id + ".json"
     fs_write(tmp_path, snapshot_data)
     engram_load(tmp_path)
@@ -369,6 +449,7 @@ load_identity_context()
 seed_persona_from_env()
 let boot_num: Int = mem_boot_count_inc()
 state_set("soul_boot_count", int_to_str(boot_num))
+state_set("soul_boot_ts", int_to_str(time_now()))
 println("[soul] boot #" + int_to_str(boot_num))
 emit_session_start_event()