@cleocode/core 2026.10.3 → 2026.10.5-rc.ci.672

package/dist/memory/dialectic-evaluator.js.map

@@ -1 +1 @@
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package/dist/memory/embedding-backfill.d.ts

@@ -0,0 +1,70 @@
+/**
+ * Bounded background embedding backfill (T13126).
+ *
+ * A one-shot process stores observations unembedded (see `brain-host.ts`).
+ * This helper embeds a bounded batch of them, loading the model once for the
+ * batch instead of once per observe. It runs from:
+ * - the detached `cleo session end` worker, once per session;
+ * - the sentient tick, in an opted-in long-lived host.
+ *
+ * It does nothing when no observation is pending: the pending count is a plain
+ * SQL read, so the model is never loaded for an empty backlog. It runs under
+ * the governor's `background-autonomous` class, which grants a slot only when
+ * memory pressure is `ok`. A deferral skips the batch, and the next session end
+ * or tick retries.
+ *
+ * @module
+ * @task T13126
+ */
+/** Observations embedded per bounded batch unless the caller says otherwise. */
+export declare const DEFAULT_EMBEDDING_BACKFILL_LIMIT = 50;
+/** Outcome of {@link runBoundedEmbeddingBackfill}. */
+export interface BoundedEmbeddingBackfillResult {
+    /** Whether a batch ran (the model was asked to embed). */
+    readonly ran: boolean;
+    /** Why no batch ran, when {@link ran} is `false`. */
+    readonly skipped?: 'none-pending' | 'deferred' | 'unavailable';
+    /** Unembedded observations found before the batch. */
+    readonly pending: number;
+    /** Observations embedded by this batch. */
+    readonly processed: number;
+    /** Observations that failed to embed in this batch. */
+    readonly errors: number;
+}
+/** Options for {@link runBoundedEmbeddingBackfill}. */
+export interface BoundedEmbeddingBackfillOptions {
+    /**
+     * Maximum observations to embed, newest first.
+     * @defaultValue {@link DEFAULT_EMBEDDING_BACKFILL_LIMIT}
+     */
+    readonly limit?: number;
+}
+/**
+ * Count observations that have a narrative but no embedding yet.
+ *
+ * A plain SQL read: it never loads the embedding model.
+ *
+ * @param projectRoot - Project root directory.
+ * @returns The pending count, or `0` when the brain store or its vector table
+ *   is unavailable.
+ */
+export declare function countUnembeddedObservations(projectRoot: string): Promise<number>;
+/**
+ * Embed a bounded batch of unembedded observations, when any exist and the
+ * governor admits background work.
+ *
+ * Never throws: the backfill is best-effort enrichment of rows that are already
+ * stored and findable by BM25.
+ *
+ * @param projectRoot - Project root directory.
+ * @param options - Batch bound.
+ * @returns What ran and how many rows were embedded.
+ *
+ * @example
+ * ```ts
+ * const r = await runBoundedEmbeddingBackfill('/my/project', { limit: 50 });
+ * if (r.ran) console.log(`embedded ${r.processed} of ${r.pending}`);
+ * ```
+ */
+export declare function runBoundedEmbeddingBackfill(projectRoot: string, options?: BoundedEmbeddingBackfillOptions): Promise<BoundedEmbeddingBackfillResult>;
+//# sourceMappingURL=embedding-backfill.d.ts.map

package/dist/memory/embedding-backfill.d.ts.map

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package/dist/memory/embedding-backfill.js

@@ -0,0 +1,110 @@
+/**
+ * Bounded background embedding backfill (T13126).
+ *
+ * A one-shot process stores observations unembedded (see `brain-host.ts`).
+ * This helper embeds a bounded batch of them, loading the model once for the
+ * batch instead of once per observe. It runs from:
+ * - the detached `cleo session end` worker, once per session;
+ * - the sentient tick, in an opted-in long-lived host.
+ *
+ * It does nothing when no observation is pending: the pending count is a plain
+ * SQL read, so the model is never loaded for an empty backlog. It runs under
+ * the governor's `background-autonomous` class, which grants a slot only when
+ * memory pressure is `ok`. A deferral skips the batch, and the next session end
+ * or tick retries.
+ *
+ * @module
+ * @task T13126
+ */
+import { getLogger } from '../logger.js';
+/** Set after the first pending-count failure is logged at warn. */
+let countFailureWarned = false;
+/** Observations embedded per bounded batch unless the caller says otherwise. */
+export const DEFAULT_EMBEDDING_BACKFILL_LIMIT = 50;
+/**
+ * Count observations that have a narrative but no embedding yet.
+ *
+ * A plain SQL read: it never loads the embedding model.
+ *
+ * @param projectRoot - Project root directory.
+ * @returns The pending count, or `0` when the brain store or its vector table
+ *   is unavailable.
+ */
+export async function countUnembeddedObservations(projectRoot) {
+    try {
+        const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
+        await getBrainDb(projectRoot);
+        const nativeDb = getBrainNativeDb(projectRoot);
+        if (!nativeDb)
+            return 0;
+        const { typedGet } = await import('../store/typed-query.js');
+        const row = typedGet(nativeDb.prepare(`
+        SELECT COUNT(*) AS n
+        FROM main.brain_observations o
+        LEFT JOIN main.brain_embeddings e ON o.id = e.id
+        WHERE e.id IS NULL AND o.narrative IS NOT NULL
+      `));
+        return row?.n ?? 0;
+    }
+    catch (err) {
+        // Warn once per process so a permanently broken vector table is visible,
+        // then stay at debug (the backfill runs every tick and session end).
+        const log = getLogger('embedding-backfill');
+        const record = { err, projectRoot };
+        const msg = 'Unembedded observation count unavailable; skipping the backfill';
+        if (countFailureWarned)
+            log.debug(record, msg);
+        else {
+            countFailureWarned = true;
+            log.warn(record, msg);
+        }
+        return 0;
+    }
+}
+/**
+ * Embed a bounded batch of unembedded observations, when any exist and the
+ * governor admits background work.
+ *
+ * Never throws: the backfill is best-effort enrichment of rows that are already
+ * stored and findable by BM25.
+ *
+ * @param projectRoot - Project root directory.
+ * @param options - Batch bound.
+ * @returns What ran and how many rows were embedded.
+ *
+ * @example
+ * ```ts
+ * const r = await runBoundedEmbeddingBackfill('/my/project', { limit: 50 });
+ * if (r.ran) console.log(`embedded ${r.processed} of ${r.pending}`);
+ * ```
+ */
+export async function runBoundedEmbeddingBackfill(projectRoot, options = {}) {
+    const log = getLogger('embedding-backfill');
+    const pending = await countUnembeddedObservations(projectRoot);
+    if (pending === 0)
+        return { ran: false, skipped: 'none-pending', pending, processed: 0, errors: 0 };
+    const { admitFailOpen, governor } = await import('../resources/governor.js');
+    const { admission } = await admitFailOpen('background-autonomous', () => governor.tryAcquire('background-autonomous'));
+    if (admission.deferred) {
+        log.debug({ projectRoot, pending, retryAfterMs: admission.retryAfterMs }, 'Embedding backfill deferred by the governor');
+        return { ran: false, skipped: 'deferred', pending, processed: 0, errors: 0 };
+    }
+    try {
+        const { populateEmbeddings } = await import('./retrieval/observe.js');
+        const result = await populateEmbeddings(projectRoot, {
+            limit: options.limit ?? DEFAULT_EMBEDDING_BACKFILL_LIMIT,
+        });
+        if (result.inactiveReason !== undefined) {
+            return { ran: false, skipped: 'unavailable', pending, processed: 0, errors: 0 };
+        }
+        return { ran: true, pending, processed: result.processed, errors: result.errors };
+    }
+    catch (err) {
+        log.warn({ err, projectRoot }, 'Embedding backfill failed; rows stay BM25-only');
+        return { ran: true, pending, processed: 0, errors: 1 };
+    }
+    finally {
+        await admission.release();
+    }
+}
+//# sourceMappingURL=embedding-backfill.js.map

package/dist/memory/embedding-backfill.js.map

@@ -0,0 +1 @@
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package/dist/memory/index.js

@@ -7,7 +7,7 @@
  */
 import { existsSync, readFileSync } from 'node:fs';
 import { join, resolve } from 'node:path';
-import { ExitCode } from '@cleocode/contracts';
+import { ExitCode } from '@cleocode/contracts/exit-codes.js';
 import { CleoError } from '../errors.js';
 import { getBackupDir, getManifestPath as getCentralManifestPath, getProjectRoot, resolveCleoDir, } from '../paths.js';
 import { safeReadFile } from '../store/atomic.js';

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package/dist/memory/manifest-identity.js

@@ -21,7 +21,7 @@
  */
 import { closeSync, constants as fsConstants, fstatSync, openSync, readFileSync, realpathSync, statSync, } from 'node:fs';
 import { isAbsolute, join, relative, sep } from 'node:path';
-import { isStorableTaskId, isTaskId } from '@cleocode/contracts';
+import { isStorableTaskId, isTaskId } from '@cleocode/contracts/task-id.js';
 /** Longest accepted manifest entry id. */
 export const MANIFEST_ENTRY_ID_MAX_LENGTH = 200;
 /**

package/dist/memory/manifest-identity.js.map

@@ -1 +1 @@
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+{"version":3,"file":"manifest-identity.js","sourceRoot":"","sources":["../../src/memory/manifest-identity.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH,OAAO,EACL,SAAS,EACT,SAAS,IAAI,WAAW,EACxB,SAAS,EACT,QAAQ,EACR,YAAY,EACZ,YAAY,EACZ,QAAQ,GACT,MAAM,SAAS,CAAC;AACjB,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,WAAW,CAAC;AAC5D,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAC;AAE5E,0CAA0C;AAC1C,MAAM,CAAC,MAAM,4BAA4B,GAAG,GAAG,CAAC;AAEhD;;;;;GAKG;AACH,MAAM,CAAC,MAAM,yBAAyB,GAAG,iCAAiC,CAAC;AAE3E,yCAAyC;AACzC,MAAM,CAAC,MAAM,wBAAwB,GAAG,IAAI,CAAC;AAE7C,wFAAwF;AACxF,MAAM,CAAC,MAAM,+BAA+B,GAAG,GAAG,CAAC;AAEnD,wFAAwF;AACxF,MAAM,aAAa,GAAG,qBAAqB,CAAC;AAE5C,kGAAkG;AAClG,MAAM,aAAa,GAAG,UAAU,CAAC;AAEjC,oEAAoE;AACpE,MAAM,aAAa,GAAG,WAAW,CAAC;AAElC,qEAAqE;AACrE,MAAM,aAAa,GAAG,iBAAiB,CAAC;AAExC;;;;GAIG;AACH,MAAM,kBAAkB,GAAG,oBAAoB,CAAC;AAEhD;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAAC,KAAc;IAC7C,IAAI,QAAQ,CAAC,KAAK,CAAC;QAAE,OAAO,IAAI,CAAC;IACjC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,gBAAgB,CAAC,KAAK,CAAC,IAAI,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AAChG,CAAC;AAcD;;;;;GAKG;AACH,SAAS,OAAO,CAAC,KAAa;IAC5B,OAAO,KAAK,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,MAAM,SAAS,CAAC;AACzF,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,sBAAsB,CAAC,EAAW;IAChD,IAAI,OAAO,EAAE,KAAK,QAAQ,IAAI,EAAE,KAAK,EAAE;QAAE,OAAO,+BAA+B,CAAC;IAChF,IAAI,EAAE,CAAC,MAAM,GAAG,4BAA4B,EAAE,CAAC;QAC7C,OAAO,SAAS,EAAE,CAAC,MAAM,+BAA+B,4BAA4B,EAAE,CAAC;IACzF,CAAC;IACD,IAAI,CAAC,yBAAyB,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC;QACxC,OAAO,uFAAuF,CAAC;IACjG,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;;;;;;;;;;;;GAaG;AACH,MAAM,UAAU,mBAAmB,CAAC,IAAa,EAAE,IAAY;IAC7D,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,IAAI,KAAK,EAAE;QAAE,OAAO,iCAAiC,CAAC;IACtF,IAAI,IAAI,CAAC,MAAM,GAAG,wBAAwB,EAAE,CAAC;QAC3C,OAAO,WAAW,IAAI,CAAC,MAAM,+BAA+B,wBAAwB,EAAE,CAAC;IACzF,CAAC;IACD,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,0CAA0C,CAAC;IAChF,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,6BAA6B,CAAC;IACnE,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;QAAE,OAAO,mCAAmC,CAAC;IACpE,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,uCAAuC,CAAC;IAC7E,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,UAAU,CAAC,IAAI,CAAC;QAAE,OAAO,8BAA8B,CAAC;IACpF,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC;IAC1C,MAAM,OAAO,GAAG,IAAI;SACjB,KAAK,CAAC,OAAO,CAAC;SACd,IAAI,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,OAAO,EAAE,MAAM,CAAC,GAAG,+BAA+B,CAAC,CAAC;IAC3F,IAAI,OAAO,KAAK,SAAS,EAAE,CAAC;QAC1B,OAAO,uCAAuC,+BAA+B,QAAQ,CAAC;IACxF,CAAC;IACD,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC,CAAC;IAC7C,IAAI,GAAG,KAAK,EAAE,IAAI,GAAG,KAAK,IAAI,IAAI,GAAG,CAAC,UAAU,CAAC,KAAK,GAAG,EAAE,CAAC,IAAI,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QAChF,OAAO,gDAAgD,CAAC;IAC1D,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,sBAAsB,CACpC,KAA+D,EAC/D,IAAY;IAEZ,MAAM,MAAM,GAA4B,EAAE,CAAC;IAC3C,MAAM,SAAS,GAAG,sBAAsB,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACnD,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,CAAC,IAAI,CAAC;YACV,KAAK,EAAE,IAAI;YACX,IAAI,EAAE,cAAc;YACpB,KAAK,EAAE,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC;YACtC,OAAO,EAAE,SAAS;SACnB,CAAC,CAAC;IACL,CAAC;IACD,IAAI,KAAK,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;QACrC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,YAAY,CAAC,EAAE,CAAC;YACvC,MAAM,CAAC,IAAI,CAAC;gBACV,KAAK,EAAE,cAAc;gBACrB,IAAI,EAAE,cAAc;gBACpB,KAAK,EAAE,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;gBAC1C,OAAO,EAAE,2CAA2C;aACrD,CAAC,CAAC;QACL,CAAC;aAAM,CAAC;YACN,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,YAAY,EAAE,CAAC;gBACxC,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,EAAE,CAAC;oBAC9B,MAAM,CAAC,IAAI,CAAC;wBACV,KAAK,EAAE,cAAc;wBACrB,IAAI,EAAE,cAAc;wBACpB,KAAK,EAAE,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;wBAC9B,OAAO,EAAE,gDAAgD;qBAC1D,CAAC,CAAC;gBACL,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,uFAAuF;IACvF,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,mBAAmB,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC;IAC5F,IAAI,WAAW,EAAE,CAAC;QAChB,MAAM,CAAC,IAAI,CAAC;YACV,KAAK,EAAE,MAAM;YACb,IAAI,EAAE,cAAc;YACpB,KAAK,EAAE,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC;YACxC,OAAO,EAAE,WAAW;SACrB,CAAC,CAAC;IACL,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,sBAAsB,CAC1C,OAA0B,EAC1B,WAAmB;IAEnB,MAAM,UAAU,GAAG,CAAC,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;IAC9E,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IACvC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,MAAM,CAAC,2BAA2B,CAAC,CAAC;IACtE,MAAM,QAAQ,GAAG,MAAM,eAAe,CAAC,WAAW,CAAC,CAAC;IACpD,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,KAAK,MAAM,EAAE,IAAI,UAAU,EAAE,CAAC;QAC5B,IAAI,CAAC,CAAC,MAAM,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC,CAAC;YAAE,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACzD,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAiBD;;;;;GAKG;AACH,SAAS,SAAS,CAAC,KAAc;IAC/B,OAAO,KAAK,YAAY,KAAK,IAAI,MAAM,IAAI,KAAK,IAAI,OAAO,KAAK,CAAC,IAAI,KAAK,QAAQ;QAChF,CAAC,CAAC,KAAK,CAAC,IAAI;QACZ,CAAC,CAAC,SAAS,CAAC;AAChB,CAAC;AAED,+EAA+E;AAC/E,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC,CAAC;AAEvD;;;;;;;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package/dist/memory/retrieval/observe.d.ts

@@ -4,6 +4,7 @@
  * @task T5134
  * @epic T5149
  */
+import type { DatabaseSync } from 'node:sqlite';
 import type { ObserveBrainParams, ObserveBrainResult } from '@cleocode/contracts';
 import type { OperationExecutionContext } from '@cleocode/contracts/jobs';
 /**
@@ -39,6 +40,22 @@ import type { OperationExecutionContext } from '@cleocode/contracts/jobs';
  * ```
  */
 export declare function observeBrain(projectRoot: string, params: ObserveBrainParams, execution?: OperationExecutionContext): Promise<ObserveBrainResult>;
+/**
+ * Upsert computed embeddings into `brain_embeddings` on the given handle.
+ *
+ * Callers must be the brain single-writer chokepoint: the `embed` write op's
+ * handler (`brain-writer-handlers.ts`, worker or inline under the lease and
+ * mutex) and the host's observe-time embed, which runs inside the writer.
+ *
+ * @param nativeDb - The writer's brain handle.
+ * @param rows - Observation ids and their vectors.
+ * @returns Rows written.
+ * @task T13218
+ */
+export declare function upsertEmbeddingRowsNative(nativeDb: DatabaseSync, rows: ReadonlyArray<{
+    id: string;
+    vector: Float32Array;
+}>): number;
 /** Result from populateEmbeddings backfill. */
 export interface PopulateEmbeddingsResult {
     processed: number;
@@ -73,6 +90,12 @@ export interface PopulateEmbeddingsResult {
 export interface PopulateEmbeddingsOptions {
     /** Maximum items processed per batch cycle. Defaults to 50. */
     batchSize?: number;
+    /**
+     * Maximum observations embedded by this call, newest first (T13126). Bounds a
+     * background batch so it cannot run for the whole backlog at once.
+     * @defaultValue undefined — every unembedded observation.
+     */
+    limit?: number;
     /**
      * Progress callback invoked after each observation is attempted.
      * `current` is the 1-based count of observations attempted so far;

package/dist/memory/retrieval/observe.d.ts.map

@@ -1 +1 @@
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package/dist/memory/retrieval/observe.js

@@ -12,6 +12,7 @@ import { sessionExistsInTasksDb, sessionExistsInTasksDbFresh, } from '../../stor
 import { getBrainAccessor } from '../../store/memory-accessor.js';
 import { getDb } from '../../store/sqlite.js';
 import { embedText, ensureEmbeddingProvider, isEmbeddingAvailable } from '../brain-embedding.js';
+import { isBrainWriterIsolate, isLongLivedBrainHost } from '../brain-host.js';
 import { addGraphEdge, upsertGraphNode } from '../graph-auto-populate.js';
 import { classifyObservationTypeByKeywords, } from '../observation-type-decision.js';
 import { computeObservationQuality } from '../quality-scoring.js';
@@ -307,32 +308,43 @@ export async function observeBrain(projectRoot, params, execution) {
         // into a false failure for the already-durable observation.
         return { id: row.id, type: row.type, createdAt: row.createdAt };
     }
-    // Populate embedding for this observation (T5387).
-    // Fire-and-forget: embedding runs in the background so it never blocks the CLI.
-    // T12314: the availability check used to happen HERE, before the deferred
-    // provider registration had run, so a write early in a process saw no
-    // provider and silently skipped embedding the observation it had just
-    // stored. The check now happens inside the deferred work, after ensuring a
-    // provider exists — registration is free, and the model load is bounded by
-    // the same fire-and-forget contract as before.
-    setImmediate(() => {
-        void (async () => {
-            try {
-                if (!(await ensureEmbeddingProvider()))
-                    return;
-                const vector = await embedText(text);
-                if (vector && nativeDb) {
-                    nativeDb
-                        // replace-allowed: brain_embeddings is a vec0 virtual table — never an FK parent, and virtual tables reject UPSERT (T12787)
-                        .prepare('INSERT OR REPLACE INTO brain_embeddings (id, embedding) VALUES (?, ?)')
-                        .run(id, Buffer.from(vector.buffer));
+    // Populate embedding for this observation (T5387) — in a long-lived host only.
+    // T13126: loading the local embedding model costs ~280 MB, and a one-shot
+    // process paid it on every observe for a single vector. A one-shot process
+    // now leaves the row unembedded; `populateEmbeddings` fills it later (an
+    // opted-in host's tick, the `cleo session end` background batch, or
+    // `cleo backfill`). Until then the observation is found by BM25/FTS5 only.
+    // T12314: the availability check happens inside the deferred work, after
+    // ensuring a provider exists — registration is free.
+    if (isLongLivedBrainHost()) {
+        setImmediate(() => {
+            void (async () => {
+                try {
+                    if (!(await ensureEmbeddingProvider()))
+                        return;
+                    const vector = await embedText(text);
+                    if (!vector)
+                        return;
+                    // T13230: inside the writer isolate this IS the chokepoint's handle,
+                    // so write directly (enqueueBrainWrite there would start a nested
+                    // manager). Anywhere else (a main thread whose host ran observeBrain
+                    // inline, or any other worker thread, T13246) the op has already
+                    // released the lease and the mutex, so the write goes back through
+                    // the chokepoint.
+                    if (isBrainWriterIsolate()) {
+                        if (nativeDb)
+                            upsertEmbeddingRowsNative(nativeDb, [{ id, vector }]);
+                        return;
+                    }
+                    const { enqueueBrainWrite } = await import('../brain-writer-thread.js');
+                    await enqueueBrainWrite({ kind: 'embed', projectRoot, rows: [{ id, vector }] });
                 }
-            }
-            catch {
-                // Silently skip embedding failures — observation is already persisted
-            }
-        })();
-    });
+                catch {
+                    // Silently skip embedding failures — observation is already persisted
+                }
+            })();
+        });
+    }
     // Regenerate memory bridge for high-value observation types (T5240).
     // Only learning and decision types trigger bridge refresh to avoid excessive writes.
     if (type === 'decision') {
@@ -367,6 +379,32 @@ export async function observeBrain(projectRoot, params, execution) {
         createdAt: row.createdAt,
     };
 }
+// ============================================================================
+// Embedding Backfill Pipeline (T5387)
+// ============================================================================
+/**
+ * Upsert computed embeddings into `brain_embeddings` on the given handle.
+ *
+ * Callers must be the brain single-writer chokepoint: the `embed` write op's
+ * handler (`brain-writer-handlers.ts`, worker or inline under the lease and
+ * mutex) and the host's observe-time embed, which runs inside the writer.
+ *
+ * @param nativeDb - The writer's brain handle.
+ * @param rows - Observation ids and their vectors.
+ * @returns Rows written.
+ * @task T13218
+ */
+export function upsertEmbeddingRowsNative(nativeDb, rows) {
+    const stmt = nativeDb
+        // replace-allowed: brain_embeddings is a vec0 virtual table — never an FK parent, and virtual tables reject UPSERT (T12787)
+        .prepare('INSERT OR REPLACE INTO brain_embeddings (id, embedding) VALUES (?, ?)');
+    let written = 0;
+    for (const row of rows) {
+        stmt.run(row.id, Buffer.from(row.vector.buffer, row.vector.byteOffset, row.vector.byteLength));
+        written++;
+    }
+    return written;
+}
 /**
  * Backfill embeddings for existing observations that lack them.
  *
@@ -433,25 +471,24 @@ export async function populateEmbeddings(projectRoot, options) {
     FROM brain_observations o
     LEFT JOIN brain_embeddings e ON o.id = e.id
     WHERE e.id IS NULL AND o.narrative IS NOT NULL
-    ORDER BY o.created_at DESC
-  `));
+    ORDER BY o.created_at DESC${options?.limit !== undefined ? ' LIMIT ?' : ''}
+  `), ...(options?.limit !== undefined ? [Math.max(0, Math.floor(options.limit))] : []));
     const total = rows.length;
     let attempted = 0;
+    // T13218: inference runs here, outside the chokepoint; the writes go through
+    // it, one `embed` op per batch, so this never writes on a second handle
+    // beside the brain writer (worker in a host, lease + mutex elsewhere).
+    const { enqueueBrainWrite } = await import('../brain-writer-thread.js');
     for (let i = 0; i < rows.length; i += batchSize) {
         const batch = rows.slice(i, i + batchSize);
+        const computed = [];
         for (const row of batch) {
             try {
                 const vector = await embedText(row.narrative || row.title);
-                if (vector) {
-                    nativeDb
-                        // replace-allowed: brain_embeddings is a vec0 virtual table — never an FK parent, and virtual tables reject UPSERT (T12787)
-                        .prepare('INSERT OR REPLACE INTO brain_embeddings (id, embedding) VALUES (?, ?)')
-                        .run(row.id, Buffer.from(vector.buffer));
-                    processed++;
-                }
-                else {
+                if (vector)
+                    computed.push({ id: row.id, vector });
+                else
                     skipped++;
-                }
             }
             catch {
                 errors++;
@@ -459,6 +496,15 @@ export async function populateEmbeddings(projectRoot, options) {
             attempted++;
             onProgress?.(attempted, total);
         }
+        if (computed.length === 0)
+            continue;
+        try {
+            const result = await enqueueBrainWrite({ kind: 'embed', projectRoot, rows: computed });
+            processed += result.kind === 'embed' ? result.written : 0;
+        }
+        catch {
+            errors += computed.length;
+        }
     }
     return { processed, skipped, errors };
 }