nlm-memory 0.20.0 → 0.21.0

package/dist/core/storage/pg-storage.d.ts

@@ -1,20 +1,21 @@
 /**
  * PgStorage — canonical Storage adapter for PostgreSQL + pgvector.
  *
- * Implements the Storage port (init/close/withTransaction). withTransaction
- * uses the write-queue pattern: the sync callback queues SQL ops, then
- * PgStorage flushes the queue inside a single BEGIN/COMMIT after the
- * callback returns.
+ * Implements the Storage port (init/close). Adapter methods manage atomicity
+ * internally via explicit BEGIN/COMMIT on a PoolClient.
  *
  * pgPool() is a deprecated escape hatch for callers not yet ported to the
  * Storage interface. Tracked for removal in #215a (PG branch).
  */
 import { Pool } from "pg";
-import type { Storage, StorageContext } from "../../ports/storage.js";
+import type { Storage } from "../../ports/storage.js";
+import { PgEntityStore } from "./pg-entity-store.js";
 import { PgFactStore } from "./pg-fact-store.js";
 import { PgSessionStore } from "./pg-session-store.js";
 import { PgSignalStore } from "./pg-signal-store.js";
 import { PgCodeExemplarStore } from "./pg-code-exemplar-store.js";
+import { PgWorkstreamStore } from "./pg-workstream-store.js";
+import { PgEmbeddingConfigStore } from "./pg-embedding-config.js";
 import { PgSourceRegistry } from "../sources/source-registry.js";
 import { PgProviderRegistry } from "../providers/provider-registry.js";
 export interface PgStorageOptions {
@@ -26,16 +27,17 @@ export declare class PgStorage implements Storage {
     readonly sessions: PgSessionStore;
     readonly signals: PgSignalStore;
     readonly exemplars: PgCodeExemplarStore;
+    readonly workstreams: PgWorkstreamStore;
+    readonly entities: PgEntityStore;
+    readonly embeddingConfig: PgEmbeddingConfigStore;
     readonly sources: PgSourceRegistry;
     readonly providers: PgProviderRegistry;
     private readonly _pool;
     private readonly _migrationsDir;
-    private inTxn;
     private constructor();
     static create(opts: PgStorageOptions): PgStorage;
     init(): Promise<void>;
     close(): Promise<void>;
-    withTransaction<T>(fn: (ctx: StorageContext) => T): Promise<T>;
     /**
      * Raw pool accessor. The #215a escape-hatch callers (registries, actions,
      * scheduler, ingest, backfill) have all been ported to the Storage port /

package/dist/core/storage/pg-storage.js

@@ -1,22 +1,21 @@
 /**
  * PgStorage — canonical Storage adapter for PostgreSQL + pgvector.
  *
- * Implements the Storage port (init/close/withTransaction). withTransaction
- * uses the write-queue pattern: the sync callback queues SQL ops, then
- * PgStorage flushes the queue inside a single BEGIN/COMMIT after the
- * callback returns.
+ * Implements the Storage port (init/close). Adapter methods manage atomicity
+ * internally via explicit BEGIN/COMMIT on a PoolClient.
  *
  * pgPool() is a deprecated escape hatch for callers not yet ported to the
  * Storage interface. Tracked for removal in #215a (PG branch).
  */
-import { Pool } from "pg";
-import { readFileSync } from "node:fs";
-import { join } from "node:path";
+import { Pool, TypeOverrides } from "pg";
+import { runMigrationsPg } from "./pg-migrate.js";
+import { PgEntityStore } from "./pg-entity-store.js";
 import { PgFactStore } from "./pg-fact-store.js";
 import { PgSessionStore } from "./pg-session-store.js";
 import { PgSignalStore } from "./pg-signal-store.js";
 import { PgCodeExemplarStore } from "./pg-code-exemplar-store.js";
-import { PgTxBoundFactStore, PgTxBoundSessionStore } from "./pg-tx-context.js";
+import { PgWorkstreamStore } from "./pg-workstream-store.js";
+import { PgEmbeddingConfigStore } from "./pg-embedding-config.js";
 import { PgSourceRegistry } from "../sources/source-registry.js";
 import { PgProviderRegistry } from "../providers/provider-registry.js";
 export class PgStorage {
@@ -24,12 +23,13 @@ export class PgStorage {
     sessions;
     signals;
     exemplars;
+    workstreams;
+    entities;
+    embeddingConfig;
     sources;
     providers;
     _pool;
     _migrationsDir;
-    // Guards against re-entrant (synchronous) nesting only. Not concurrent-call-safe.
-    inTxn = false;
     constructor(pool, migrationsDir) {
         this._pool = pool;
         this._migrationsDir = migrationsDir;
@@ -37,57 +37,27 @@ export class PgStorage {
         this.sessions = new PgSessionStore(pool);
         this.signals = new PgSignalStore(pool);
         this.exemplars = new PgCodeExemplarStore(pool);
+        this.workstreams = new PgWorkstreamStore(pool);
+        this.entities = new PgEntityStore(pool);
+        this.embeddingConfig = new PgEmbeddingConfigStore(pool);
         this.sources = new PgSourceRegistry(pool);
         this.providers = new PgProviderRegistry(pool);
     }
     static create(opts) {
-        const pool = new Pool({ connectionString: opts.connectionString });
+        const types = new TypeOverrides();
+        const isoParser = (val) => new Date(val).toISOString();
+        types.setTypeParser(1184, isoParser); // TIMESTAMPTZ
+        types.setTypeParser(1114, isoParser); // TIMESTAMP
+        const pool = new Pool({ connectionString: opts.connectionString, types });
         return new PgStorage(pool, opts.migrationsDir);
     }
     async init() {
-        const sql = readFileSync(join(this._migrationsDir, "001_initial.sql"), "utf8");
-        await this._pool.query(sql);
+        await runMigrationsPg(this._pool, this._migrationsDir);
+        await this.embeddingConfig.load();
     }
     async close() {
         await this._pool.end();
     }
-    async withTransaction(fn) {
-        if (this.inTxn) {
-            throw new Error("PgStorage.withTransaction does not support nesting");
-        }
-        this.inTxn = true;
-        const queue = [];
-        const txFacts = new PgTxBoundFactStore(queue);
-        const txSessions = new PgTxBoundSessionStore(queue);
-        const ctx = { facts: txFacts, sessions: txSessions };
-        let result;
-        try {
-            result = fn(ctx);
-        }
-        catch (err) {
-            this.inTxn = false;
-            throw err;
-        }
-        this.inTxn = false;
-        if (queue.length > 0) {
-            const client = await this._pool.connect();
-            try {
-                await client.query("BEGIN");
-                for (const op of queue) {
-                    await client.query(op.sql, op.params);
-                }
-                await client.query("COMMIT");
-            }
-            catch (err) {
-                await client.query("ROLLBACK");
-                throw err;
-            }
-            finally {
-                client.release();
-            }
-        }
-        return result;
-    }
     /**
      * Raw pool accessor. The #215a escape-hatch callers (registries, actions,
      * scheduler, ingest, backfill) have all been ported to the Storage port /

package/dist/core/storage/pg-storage.js.map

@@ -1 +1 @@
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package/dist/core/storage/pg-workstream-store.d.ts

@@ -0,0 +1,25 @@
+import type { Pool } from "pg";
+import type { WorkstreamStore } from "../../ports/workstream-store.js";
+import { type Workstream } from "../workstream/model.js";
+export declare class PgWorkstreamStore implements WorkstreamStore {
+    private readonly pool;
+    constructor(pool: Pool);
+    create(input: {
+        id: string;
+        label: string;
+        scope: string | null;
+    }): Promise<Workstream>;
+    getById(id: string): Promise<Workstream | null>;
+    findByNormalizedLabel(normalizedLabel: string): Promise<Workstream | null>;
+    listAll(): Promise<ReadonlyArray<Workstream>>;
+    touchLastSession(id: string, atIso: string): Promise<void>;
+    setLabel(id: string, label: string): Promise<void>;
+    setStatus(id: string, status: Workstream["status"]): Promise<void>;
+    merge(fromId: string, intoId: string): Promise<void>;
+    upsertEntities(workstreamId: string, entities: ReadonlyArray<string>): Promise<void>;
+    entitiesFor(workstreamIds: ReadonlyArray<string>): Promise<Map<string, string[]>>;
+    candidatesByEntityOverlap(entities: ReadonlyArray<string>, limit: number): Promise<ReadonlyArray<{
+        workstreamId: string;
+        entities: string[];
+    }>>;
+}

package/dist/core/storage/pg-workstream-store.js

@@ -0,0 +1,97 @@
+import { normalizeLabel } from "../workstream/model.js";
+const rowToWorkstream = (r) => ({
+    id: r.id, label: r.label, status: r.status, mergedInto: r.merged_into,
+    createdAt: r.created_at, updatedAt: r.updated_at, lastSessionAt: r.last_session_at,
+    scope: r.scope,
+});
+export class PgWorkstreamStore {
+    pool;
+    constructor(pool) {
+        this.pool = pool;
+    }
+    async create(input) {
+        await this.pool.query("INSERT INTO workstreams (id, label, scope) VALUES ($1, $2, $3)", [input.id, input.label, input.scope]);
+        return (await this.getById(input.id));
+    }
+    async getById(id) {
+        const r = await this.pool.query("SELECT * FROM workstreams WHERE id = $1", [id]);
+        return r.rows[0] ? rowToWorkstream(r.rows[0]) : null;
+    }
+    async findByNormalizedLabel(normalizedLabel) {
+        const r = await this.pool.query("SELECT * FROM workstreams");
+        const hit = r.rows.find((row) => normalizeLabel(row.label) === normalizedLabel);
+        return hit ? rowToWorkstream(hit) : null;
+    }
+    async listAll() {
+        const r = await this.pool.query("SELECT * FROM workstreams");
+        return r.rows.map(rowToWorkstream);
+    }
+    async touchLastSession(id, atIso) {
+        await this.pool.query("UPDATE workstreams SET last_session_at = $1, updated_at = NOW() WHERE id = $2", [atIso, id]);
+    }
+    async setLabel(id, label) {
+        await this.pool.query("UPDATE workstreams SET label = $1, updated_at = NOW() WHERE id = $2", [label, id]);
+    }
+    async setStatus(id, status) {
+        await this.pool.query("UPDATE workstreams SET status = $1, updated_at = NOW() WHERE id = $2", [status, id]);
+    }
+    async merge(fromId, intoId) {
+        // Pointer first (source of truth for resolution), then derived entity union, then clear.
+        const client = await this.pool.connect();
+        try {
+            await client.query("BEGIN");
+            await client.query("UPDATE workstreams SET merged_into = $1, status = 'merged', updated_at = NOW() WHERE id = $2", [intoId, fromId]);
+            await client.query(`INSERT INTO workstream_entities (workstream_id, entity_canonical, session_count)
+         SELECT $1, entity_canonical, session_count FROM workstream_entities WHERE workstream_id = $2
+         ON CONFLICT (workstream_id, entity_canonical)
+         DO UPDATE SET session_count = workstream_entities.session_count + excluded.session_count`, [intoId, fromId]);
+            await client.query("DELETE FROM workstream_entities WHERE workstream_id = $1", [fromId]);
+            await client.query("COMMIT");
+        }
+        catch (err) {
+            await client.query("ROLLBACK");
+            throw err;
+        }
+        finally {
+            client.release();
+        }
+    }
+    async upsertEntities(workstreamId, entities) {
+        for (const raw of entities) {
+            const e = raw.trim();
+            if (!e)
+                continue;
+            await this.pool.query(`INSERT INTO workstream_entities (workstream_id, entity_canonical, session_count) VALUES ($1, $2, 1)
+         ON CONFLICT (workstream_id, entity_canonical) DO UPDATE SET session_count = workstream_entities.session_count + 1`, [workstreamId, e]);
+        }
+    }
+    async entitiesFor(workstreamIds) {
+        const out = new Map();
+        if (workstreamIds.length === 0)
+            return out;
+        const ph = workstreamIds.map((_, i) => `$${i + 1}`).join(",");
+        const r = await this.pool.query(`SELECT workstream_id, entity_canonical FROM workstream_entities WHERE workstream_id IN (${ph})`, [...workstreamIds]);
+        for (const row of r.rows) {
+            const list = out.get(row.workstream_id);
+            if (list)
+                list.push(row.entity_canonical);
+            else
+                out.set(row.workstream_id, [row.entity_canonical]);
+        }
+        return out;
+    }
+    async candidatesByEntityOverlap(entities, limit) {
+        const names = entities.map((e) => e.trim()).filter(Boolean);
+        if (names.length === 0)
+            return [];
+        const ph = names.map((_, i) => `$${i + 1}`).join(",");
+        const r = await this.pool.query(`SELECT workstream_id, COUNT(*) AS overlap FROM workstream_entities
+       WHERE entity_canonical IN (${ph}) GROUP BY workstream_id ORDER BY overlap DESC LIMIT $${names.length + 1}`, [...names, limit]);
+        const ids = r.rows.map((row) => row.workstream_id);
+        if (ids.length === 0)
+            return [];
+        const map = await this.entitiesFor(ids);
+        return ids.map((id) => ({ workstreamId: id, entities: map.get(id) ?? [] }));
+    }
+}
+//# sourceMappingURL=pg-workstream-store.js.map

package/dist/core/storage/pg-workstream-store.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pg-workstream-store.js","sourceRoot":"","sources":["../../../src/core/storage/pg-workstream-store.ts"],"names":[],"mappings":"AAEA,OAAO,EAAmB,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAQ5E,MAAM,eAAe,GAAG,CAAC,CAAQ,EAAc,EAAE,CAAC,CAAC;IACjD,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,UAAU,EAAE,CAAC,CAAC,WAAW;IACrE,SAAS,EAAE,CAAC,CAAC,UAAU,EAAE,SAAS,EAAE,CAAC,CAAC,UAAU,EAAE,aAAa,EAAE,CAAC,CAAC,eAAe;IAClF,KAAK,EAAE,CAAC,CAAC,KAAK;CACf,CAAC,CAAC;AAEH,MAAM,OAAO,iBAAiB;IACC;IAA7B,YAA6B,IAAU;QAAV,SAAI,GAAJ,IAAI,CAAM;IAAG,CAAC;IAE3C,KAAK,CAAC,MAAM,CAAC,KAA0D;QACrE,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,gEAAgE,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;QAC9H,OAAO,CAAC,MAAM,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,CAAE,CAAC;IACzC,CAAC;IAED,KAAK,CAAC,OAAO,CAAC,EAAU;QACtB,MAAM,CAAC,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAAQ,yCAAyC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;QACxF,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACvD,CAAC;IAED,KAAK,CAAC,qBAAqB,CAAC,eAAuB;QACjD,MAAM,CAAC,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAAQ,2BAA2B,CAAC,CAAC;QACpE,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,cAAc,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,eAAe,CAAC,CAAC;QAChF,OAAO,GAAG,CAAC,CAAC,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAC3C,CAAC;IAED,KAAK,CAAC,OAAO;QACX,MAAM,CAAC,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAAQ,2BAA2B,CAAC,CAAC;QACpE,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC;IACrC,CAAC;IAED,KAAK,CAAC,gBAAgB,CAAC,EAAU,EAAE,KAAa;QAC9C,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,+EAA+E,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC;IACtH,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,EAAU,EAAE,KAAa;QACtC,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,qEAAqE,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC;IAC5G,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,EAAU,EAAE,MAA4B;QACtD,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,sEAAsE,EAAE,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,CAAC;IAC9G,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,MAAc,EAAE,MAAc;QACxC,yFAAyF;QACzF,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC;QACzC,IAAI,CAAC;YACH,MAAM,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;YAC5B,MAAM,MAAM,CAAC,KAAK,CAChB,8FAA8F,EAC9F,CAAC,MAAM,EAAE,MAAM,CAAC,CACjB,CAAC;YACF,MAAM,MAAM,CAAC,KAAK,CAChB;;;kGAG0F,EAC1F,CAAC,MAAM,EAAE,MAAM,CAAC,CACjB,CAAC;YACF,MAAM,MAAM,CAAC,KAAK,CAAC,0DAA0D,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC;YACzF,MAAM,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;QAC/B,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,MAAM,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;YAC/B,MAAM,GAAG,CAAC;QACZ,CAAC;gBAAS,CAAC;YACT,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAAC,YAAoB,EAAE,QAA+B;QACxE,KAAK,MAAM,GAAG,IAAI,QAAQ,EAAE,CAAC;YAC3B,MAAM,CAAC,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC;YAAC,IAAI,CAAC,CAAC;gBAAE,SAAS;YACvC,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CACnB;2HACmH,EACnH,CAAC,YAAY,EAAE,CAAC,CAAC,CAClB,CAAC;QACJ,CAAC;IACH,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,aAAoC;QACpD,MAAM,GAAG,GAAG,IAAI,GAAG,EAAoB,CAAC;QACxC,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,GAAG,CAAC;QAC3C,MAAM,EAAE,GAAG,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC9D,MAAM,CAAC,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAC7B,2FAA2F,EAAE,GAAG,EAAE,CAAC,GAAG,aAAa,CAAC,CACrH,CAAC;QACF,KAAK,MAAM,GAAG,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC;YACzB,MAAM,IAAI,GAAG,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC;YACxC,IAAI,IAAI;gBAAE,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAC;;gBAAM,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,aAAa,EAAE,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAC,CAAC;QACrG,CAAC;QACD,OAAO,GAAG,CAAC;IACb,CAAC;IAED,KAAK,CAAC,yBAAyB,CAAC,QAA+B,EAAE,KAAa;QAC5E,MAAM,KAAK,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAC5D,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,EAAE,CAAC;QAClC,MAAM,EAAE,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QACtD,MAAM,CAAC,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,CAC7B;oCAC8B,EAAE,yDAAyD,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,EAC3G,CAAC,GAAG,KAAK,EAAE,KAAK,CAAC,CAClB,CAAC;QACF,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC;QACnD,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,EAAE,CAAC;QAChC,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC;QACxC,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,YAAY,EAAE,EAAE,EAAE,QAAQ,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC;IAC9E,CAAC;CACF"}

package/dist/core/storage/sqlite-code-exemplar-store.d.ts

@@ -31,6 +31,7 @@ export declare class SqliteCodeExemplarStore implements CodeExemplarStore {
     upsertEmbedding(exemplarId: string, vector: Float32Array): Promise<void>;
     searchByVector(queryVector: Float32Array, filter: CodeExemplarSearchFilter): Promise<ReadonlyArray<CodeExemplarHit>>;
     getById(id: string): Promise<CodeExemplar | null>;
+    listBySessions(sessionIds: ReadonlyArray<string>): Promise<ReadonlyArray<CodeExemplar>>;
     applyBucketCap(installScope: string, maxPerBucket: number): Promise<number>;
     pruneReverted(installScope: string): Promise<number>;
     setVerdict(id: string, patch: ExemplarVerdictPatch, source: ExemplarVerdictSource): Promise<ExemplarVerdictResult>;

package/dist/core/storage/sqlite-code-exemplar-store.js

@@ -129,6 +129,17 @@ export class SqliteCodeExemplarStore {
             .get(id);
         return row ? this.rowToExemplar(row) : null;
     }
+    async listBySessions(sessionIds) {
+        if (sessionIds.length === 0)
+            return [];
+        const ph = sessionIds.map(() => "?").join(",");
+        const rows = this.db
+            .prepare(`SELECT id, install_scope, signal_id, session_id, repo, model, lang,
+                task_context, code, code_hash, outcome, git_sha, survived, ts, created_at, retired_at, label_source
+         FROM code_exemplars WHERE session_id IN (${ph}) AND retired_at IS NULL ORDER BY ts ASC`)
+            .all(...sessionIds);
+        return rows.map((r) => this.rowToExemplar(r));
+    }
     async applyBucketCap(installScope, maxPerBucket) {
         const buckets = this.db
             .prepare(`SELECT DISTINCT repo, lang,
@@ -220,10 +231,10 @@ export class SqliteCodeExemplarStore {
         return this.db.prepare(`
       INSERT OR IGNORE INTO code_exemplars (
         id, install_scope, signal_id, session_id, repo, model, lang,
-        task_context, code, code_hash, outcome, git_sha, survived, ts, created_at
+        task_context, code, code_hash, outcome, git_sha, survived, scope, ts, created_at
       ) VALUES (
         @id, @install_scope, @signal_id, @session_id, @repo, @model, @lang,
-        @task_context, @code, @code_hash, @outcome, @git_sha, @survived, @ts, @created_at
+        @task_context, @code, @code_hash, @outcome, @git_sha, @survived, @scope, @ts, @created_at
       )
     `);
     }
@@ -242,6 +253,7 @@ export class SqliteCodeExemplarStore {
             outcome: inp.outcome,
             git_sha: inp.gitSha,
             survived: inp.survived,
+            scope: inp.scope,
             ts: inp.ts,
             created_at: new Date().toISOString(),
             retired_at: null,
@@ -263,6 +275,7 @@ export class SqliteCodeExemplarStore {
             outcome: row.outcome,
             gitSha: row.git_sha,
             survived: row.survived,
+            scope: row.scope ?? null,
             ts: row.ts,
             createdAt: row.created_at,
             retiredAt: row.retired_at,

package/dist/core/storage/sqlite-code-exemplar-store.js.map

@@ -1 +1 @@
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package/dist/core/storage/sqlite-embedding-config.d.ts

@@ -0,0 +1,10 @@
+import type Database from "better-sqlite3";
+import type { EmbeddingConfigStore, EmbeddingLane, EmbeddingLaneConfig } from "../embedding/embedding-config.js";
+export declare class SqliteEmbeddingConfigStore implements EmbeddingConfigStore {
+    private readonly db;
+    private readonly stmtGet;
+    private readonly stmtUpsert;
+    constructor(db: Database.Database);
+    getLane(lane: EmbeddingLane): EmbeddingLaneConfig | null;
+    upsertLane(cfg: EmbeddingLaneConfig, updatedAtIso: string): void;
+}

package/dist/core/storage/sqlite-embedding-config.js

@@ -0,0 +1,27 @@
+function rowToConfig(r) {
+    return { lane: r.lane, provider: r.provider, model: r.model, dim: r.dim };
+}
+export class SqliteEmbeddingConfigStore {
+    db;
+    stmtGet;
+    stmtUpsert;
+    constructor(db) {
+        this.db = db;
+        this.stmtGet = db.prepare("SELECT lane, provider, model, dim, updated_at FROM embedding_config WHERE lane = ?");
+        this.stmtUpsert = db.prepare(`INSERT INTO embedding_config (lane, provider, model, dim, updated_at)
+       VALUES (?, ?, ?, ?, ?)
+       ON CONFLICT(lane) DO UPDATE SET
+         provider   = excluded.provider,
+         model      = excluded.model,
+         dim        = excluded.dim,
+         updated_at = excluded.updated_at`);
+    }
+    getLane(lane) {
+        const row = this.stmtGet.get(lane);
+        return row ? rowToConfig(row) : null;
+    }
+    upsertLane(cfg, updatedAtIso) {
+        this.stmtUpsert.run(cfg.lane, cfg.provider, cfg.model, cfg.dim, updatedAtIso);
+    }
+}
+//# sourceMappingURL=sqlite-embedding-config.js.map

package/dist/core/storage/sqlite-embedding-config.js.map

@@ -0,0 +1 @@
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package/dist/core/storage/sqlite-entity-store.d.ts

@@ -0,0 +1,13 @@
+/**
+ * SqliteEntityStore -- EntityStore implementation over better-sqlite3.
+ *
+ * All merge operations run inside a single synchronous transaction so
+ * the database is never left in a partially-merged state.
+ */
+import type Database from "better-sqlite3";
+import type { EntityStore } from "../../ports/entity-store.js";
+export declare class SqliteEntityStore implements EntityStore {
+    private readonly db;
+    constructor(db: Database.Database);
+    merge(source: string, target: string): Promise<void>;
+}

package/dist/core/storage/sqlite-entity-store.js

@@ -0,0 +1,96 @@
+/**
+ * SqliteEntityStore -- EntityStore implementation over better-sqlite3.
+ *
+ * All merge operations run inside a single synchronous transaction so
+ * the database is never left in a partially-merged state.
+ */
+export class SqliteEntityStore {
+    db;
+    constructor(db) {
+        this.db = db;
+    }
+    async merge(source, target) {
+        const txn = this.db.transaction(() => {
+            const targetRow = this.db
+                .prepare("SELECT status FROM entities WHERE canonical = ?")
+                .get(target);
+            if (!targetRow)
+                throw new Error(`merge: target entity not found: ${target}`);
+            if (targetRow.status === "retired") {
+                throw new Error(`merge: target entity is retired: ${target}`);
+            }
+            const sourceRow = this.db
+                .prepare("SELECT status FROM entities WHERE canonical = ?")
+                .get(source);
+            if (!sourceRow)
+                throw new Error(`merge: source entity not found: ${source}`);
+            // Step 1: copy source session_entities to target, dedup on composite PK.
+            this.db
+                .prepare(`INSERT OR IGNORE INTO session_entities (session_id, entity_canonical)
+           SELECT session_id, ? FROM session_entities WHERE entity_canonical = ?`)
+                .run(target, source);
+            // Step 2: delete source's session_entities rows.
+            this.db
+                .prepare("DELETE FROM session_entities WHERE entity_canonical = ?")
+                .run(source);
+            // Step 3: recompute target.session_count exactly from session_entities.
+            this.db
+                .prepare(`UPDATE entities
+             SET session_count = (SELECT COUNT(*) FROM session_entities WHERE entity_canonical = ?),
+                 updated_at    = datetime('now')
+           WHERE canonical = ?`)
+                .run(target, target);
+            // Step 4: widen first_seen_session / last_seen_session.
+            // first_seen and last_seen are session IDs (text), not timestamps.
+            // We use sessions.started_at to order them chronologically and pick
+            // the earliest / latest. This is correct as long as session IDs are
+            // stable references (they are -- FK to sessions(id)).
+            const bothSeenSessions = this.db
+                .prepare(`SELECT id, started_at FROM sessions
+           WHERE id IN (
+             SELECT first_seen_session FROM entities WHERE canonical IN (?, ?)
+             UNION
+             SELECT last_seen_session  FROM entities WHERE canonical IN (?, ?)
+           )`)
+                .all(source, target, source, target);
+            if (bothSeenSessions.length > 0) {
+                bothSeenSessions.sort((a, b) => a.started_at.localeCompare(b.started_at));
+                const earliest = bothSeenSessions[0].id;
+                const latest = bothSeenSessions[bothSeenSessions.length - 1].id;
+                this.db
+                    .prepare(`UPDATE entities
+               SET first_seen_session = ?,
+                   last_seen_session  = ?,
+                   updated_at         = datetime('now')
+             WHERE canonical = ?`)
+                    .run(earliest, latest, target);
+            }
+            // Step 5: insert the variant record so future ingest resolves source -> target.
+            this.db
+                .prepare(`INSERT OR IGNORE INTO entity_variants (variant, canonical, source_session_id)
+           VALUES (?, ?, NULL)`)
+                .run(source, target);
+            // Step 6: re-point existing variants of source to target.
+            const sourceVariants = this.db
+                .prepare("SELECT variant FROM entity_variants WHERE canonical = ?")
+                .all(source);
+            for (const { variant } of sourceVariants) {
+                if (variant === source)
+                    continue;
+                this.db
+                    .prepare("UPDATE entity_variants SET canonical = ? WHERE variant = ?")
+                    .run(target, variant);
+            }
+            // Step 7: retire the source entity row in place.
+            this.db
+                .prepare(`UPDATE entities
+             SET status        = 'retired',
+                 session_count = 0,
+                 updated_at    = datetime('now')
+           WHERE canonical = ?`)
+                .run(source);
+        });
+        txn();
+    }
+}
+//# sourceMappingURL=sqlite-entity-store.js.map

package/dist/core/storage/sqlite-entity-store.js.map

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package/dist/core/storage/sqlite-fact-store.d.ts

@@ -26,20 +26,17 @@ export declare class SqliteFactStore implements FactStore {
      * other callers should reach FactStore via storage.facts.
      */
     constructor(db: Database.Database);
+    private cachedInsertStmt;
     insert(fact: Fact): Promise<void>;
     insertMany(facts: ReadonlyArray<Fact>): Promise<void>;
-    /**
-     * @internal. Sync row insert for use inside an already-open better-sqlite3
-     * transaction. Used only by SqliteSessionStore's inlined ingest blocks
-     * (which require sync execution inside the txn callback). External callers
-     * use insertMany() or ingestSessionFacts() via Storage.withTransaction.
-     */
-    insertRowInTxn(fact: Fact): void;
     getById(id: string): Promise<Fact | null>;
     getByIds(ids: ReadonlyArray<string>): Promise<ReadonlyArray<Fact>>;
     findCurrent(subject: string, predicate: string): Promise<Fact | null>;
     list(query: FactQuery): Promise<ReadonlyArray<Fact>>;
     listBySession(sessionId: string): Promise<ReadonlyArray<Fact>>;
+    listBySessions(sessionIds: ReadonlyArray<string>, opts?: {
+        includeSuperseded?: boolean;
+    }): Promise<ReadonlyArray<Fact>>;
     listForRecall(filter: FactListFilter): Promise<ReadonlyArray<Fact>>;
     semanticSearch(queryVector: Float32Array, limit: number): Promise<ReadonlyArray<FactSemanticNeighbor>>;
     getHistory(subject: string, predicate?: string): Promise<ReadonlyArray<FactHistoryChain>>;
@@ -57,6 +54,17 @@ export declare class SqliteFactStore implements FactStore {
     markSuperseded(oldId: string, newId: string | null): Promise<void>;
     retire(factId: string): Promise<void>;
     ingestSessionFacts(sessionId: string, facts: ReadonlyArray<Fact>): Promise<void>;
+    /**
+     * Sync core of ingestSessionFacts, callable from inside an existing
+     * better-sqlite3 transaction. SINGLE SOURCE OF TRUTH for the replace +
+     * deterministic-collapse + embedding-cleanup logic. The live ingest path
+     * (SqliteSessionStore.insertSession / insertFactsForSession) runs inside its
+     * own sync txn and delegates here, so it can no longer drift from this method.
+     * NLM #351's embedding-ghost (bug 1) and supersedence-cycle (bug 2) fixes
+     * originally landed only here and silently skipped the inlined copies — the
+     * path production actually uses — leaving both bugs live in production.
+     */
+    ingestSessionFactsInTxn(sessionId: string, facts: ReadonlyArray<Fact>, scope?: string | null): void;
     private insertStmt;
     private toRow;
     private rowToFact;