nlm-memory 0.12.0 → 0.13.1

package/dist/core/ingest/ingest-session.js

@@ -8,6 +8,7 @@
  */
 import { createHash } from "node:crypto";
 import { extractFacts } from "../facts/extract-facts.js";
+import { PgSessionStore } from "../storage/pg-session-store.js";
 const BODY_CAP = 200_000;
 const CONFIDENCE_FLOOR = 0.3;
 export function deriveSessionId(runtime, startedAt, text) {
@@ -62,10 +63,17 @@ export async function ingestSession(input, deps) {
         decisions: classification.decisions,
         openQuestions: classification.open,
     };
-    const factSink = deps.factStore
-        ? { factStore: deps.factStore, facts: extractFacts(classification, id, startedAt) }
-        : null;
-    await deps.store.insertSession(record, deps.embedder, null, factSink);
+    const facts = deps.factStore
+        ? extractFacts(classification, id, startedAt)
+        : [];
+    // Store + factStore come from the same backend (see buildStack); the cast
+    // is sound — TS can't correlate the two union members at one call site.
+    if (deps.store instanceof PgSessionStore) {
+        await deps.store.insertSession(record, deps.embedder, null, deps.factStore ? { factStore: deps.factStore, facts } : null);
+    }
+    else {
+        await deps.store.insertSession(record, deps.embedder, null, deps.factStore ? { factStore: deps.factStore, facts } : null);
+    }
     return { id, status: "ingested", latencyMs: Date.now() - t0, confidence: classification.confidence };
 }
 //# sourceMappingURL=ingest-session.js.map

package/dist/core/ingest/ingest-session.js.map

@@ -1 +1 @@
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package/dist/core/providers/provider-registry.d.ts

@@ -42,34 +42,54 @@ export interface ProviderUpdate {
     readonly defaultModel?: string | null;
     readonly enabled?: boolean;
 }
-export declare class ProviderRegistry {
+/**
+ * ProviderRegistryPort — the backend-agnostic provider-registry contract that
+ * SqliteStorage and PgStorage expose as `storage.providers`. Async across both
+ * backends (the SQLite impl declares async methods with sync bodies, matching
+ * the SignalStore/FactStore convention). `seedDefaults` is intentionally NOT on
+ * the port: it bridges from the local `DEEPSEEK_API_KEY` env, which is a
+ * single-user SQLite concern — seeding a hosted multi-tenant PG from one
+ * operator's env would be wrong, so the PG adapter never seeds providers.
+ */
+export interface ProviderRegistryPort {
+    list(): Promise<ProviderRow[]>;
+    get(id: number): Promise<ProviderRow | null>;
+    getByName(name: string): Promise<ProviderRow | null>;
+    getSecret(id: number): Promise<string | null>;
+    insert(input: ProviderInsert): Promise<ProviderRow>;
+    update(id: number, patch: ProviderUpdate): Promise<ProviderRow | null>;
+    delete(id: number): Promise<boolean>;
+}
+export declare class ProviderRegistry implements ProviderRegistryPort {
     private readonly db;
     constructor(db: Database.Database);
-    list(): ProviderRow[];
-    get(id: number): ProviderRow | null;
-    getByName(name: string): ProviderRow | null;
+    list(): Promise<ProviderRow[]>;
+    get(id: number): Promise<ProviderRow | null>;
+    getByName(name: string): Promise<ProviderRow | null>;
     /** Returns the secret. Use only inside the daemon — never echo to HTTP. */
-    getSecret(id: number): string | null;
-    insert(input: ProviderInsert): ProviderRow;
-    update(id: number, patch: ProviderUpdate): ProviderRow | null;
-    delete(id: number): boolean;
+    getSecret(id: number): Promise<string | null>;
+    insert(input: ProviderInsert): Promise<ProviderRow>;
+    update(id: number, patch: ProviderUpdate): Promise<ProviderRow | null>;
+    delete(id: number): Promise<boolean>;
     /**
      * Seed defaults on an empty registry. Bridges from the legacy env-var
      * setup: if DEEPSEEK_API_KEY is present, the DeepSeek row carries it
-     * forward; Ollama is always seeded since it needs no key.
+     * forward; Ollama is always seeded since it needs no key. SQLite-only —
+     * not on ProviderRegistryPort (see the port's doc comment).
      */
-    seedDefaults(): void;
+    seedDefaults(): Promise<void>;
 }
 import type { Pool } from "pg";
 /**
  * PgProviderRegistry — CRUD over `providers` for the PG storage path.
  * API mirrors ProviderRegistry exactly.
  */
-export declare class PgProviderRegistry {
+export declare class PgProviderRegistry implements ProviderRegistryPort {
     private readonly pool;
     constructor(pool: Pool);
     list(): Promise<ProviderRow[]>;
     get(id: number): Promise<ProviderRow | null>;
+    getByName(name: string): Promise<ProviderRow | null>;
     getSecret(id: number): Promise<string | null>;
     insert(input: ProviderInsert): Promise<ProviderRow>;
     update(id: number, patch: ProviderUpdate): Promise<ProviderRow | null>;

package/dist/core/providers/provider-registry.js

@@ -36,7 +36,7 @@ const DEFAULT_BASE_URLS = {
 };
 const DEFAULT_MODELS = {
     deepseek: "deepseek-v4-flash",
-    ollama: "qwen3:4b-instruct-2507-q4_K_M",
+    ollama: "qwen3.5:4b",
     openai: "gpt-4o-mini",
     anthropic: "claude-haiku-4-5-20251001",
     openrouter: "anthropic/claude-haiku-4-5",
@@ -47,24 +47,24 @@ export class ProviderRegistry {
     constructor(db) {
         this.db = db;
     }
-    list() {
+    async list() {
         const rows = this.db.prepare(`SELECT * FROM providers ORDER BY id ASC`).all();
         return rows.map((r) => rowFromDb(r, false));
     }
-    get(id) {
+    async get(id) {
         const row = this.db.prepare(`SELECT * FROM providers WHERE id = ?`).get(id);
         return row ? rowFromDb(row, false) : null;
     }
-    getByName(name) {
+    async getByName(name) {
         const row = this.db.prepare(`SELECT * FROM providers WHERE name = ?`).get(name);
         return row ? rowFromDb(row, false) : null;
     }
     /** Returns the secret. Use only inside the daemon — never echo to HTTP. */
-    getSecret(id) {
+    async getSecret(id) {
         const row = this.db.prepare(`SELECT * FROM providers WHERE id = ?`).get(id);
         return row?.api_key ?? null;
     }
-    insert(input) {
+    async insert(input) {
         const baseUrl = input.baseUrl ?? DEFAULT_BASE_URLS[input.kind];
         const defaultModel = input.defaultModel ?? DEFAULT_MODELS[input.kind];
         const result = this.db.prepare(`
@@ -79,12 +79,12 @@ export class ProviderRegistry {
             enabled: input.enabled === false ? 0 : 1,
         });
         const id = Number(result.lastInsertRowid);
-        const row = this.get(id);
+        const row = await this.get(id);
         if (!row)
             throw new Error(`ProviderRegistry.insert: row ${id} not found after insert`);
         return row;
     }
-    update(id, patch) {
+    async update(id, patch) {
         const fields = [];
         const params = { id };
         if (patch.name !== undefined) {
@@ -113,26 +113,27 @@ export class ProviderRegistry {
         this.db.prepare(`UPDATE providers SET ${fields.join(", ")} WHERE id = @id`).run(params);
         return this.get(id);
     }
-    delete(id) {
+    async delete(id) {
         const result = this.db.prepare(`DELETE FROM providers WHERE id = ?`).run(id);
         return result.changes > 0;
     }
     /**
      * Seed defaults on an empty registry. Bridges from the legacy env-var
      * setup: if DEEPSEEK_API_KEY is present, the DeepSeek row carries it
-     * forward; Ollama is always seeded since it needs no key.
+     * forward; Ollama is always seeded since it needs no key. SQLite-only —
+     * not on ProviderRegistryPort (see the port's doc comment).
      */
-    seedDefaults() {
+    async seedDefaults() {
         const count = this.db.prepare(`SELECT COUNT(*) AS c FROM providers`).get();
         if ((count?.c ?? 0) > 0)
             return;
-        this.insert({
+        await this.insert({
             kind: "ollama",
             name: "Ollama (local)",
             baseUrl: process.env["NLM_OLLAMA_URL"] ?? "http://localhost:11434",
         });
         const deepseekKey = process.env["DEEPSEEK_API_KEY"];
-        this.insert({
+        await this.insert({
             kind: "deepseek",
             name: "DeepSeek",
             apiKey: deepseekKey ?? null,
@@ -172,6 +173,19 @@ export class PgProviderRegistry {
             createdAt: r.created_at, updatedAt: r.updated_at,
         };
     }
+    async getByName(name) {
+        const result = await this.pool.query(`SELECT id, kind, name, base_url, api_key, default_model, enabled, created_at, updated_at
+       FROM providers WHERE name = $1`, [name]);
+        if (!result.rows[0])
+            return null;
+        const r = result.rows[0];
+        return {
+            id: r.id, kind: r.kind, name: r.name, baseUrl: r.base_url,
+            apiKey: null, hasApiKey: r.api_key !== null && r.api_key.length > 0,
+            defaultModel: r.default_model, enabled: r.enabled,
+            createdAt: r.created_at, updatedAt: r.updated_at,
+        };
+    }
     async getSecret(id) {
         const result = await this.pool.query("SELECT api_key FROM providers WHERE id = $1", [id]);
         return result.rows[0]?.api_key ?? null;

package/dist/core/providers/provider-registry.js.map

@@ -1 +1 @@
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package/dist/core/recall-facts/fact-recall-service.js

@@ -25,8 +25,6 @@ const DEFAULT_LIMIT = 10;
 const MAX_LIMIT = 100;
 const DEFAULT_MIN_CONFIDENCE = 0.6;
 const STORAGE_FETCH_CAP = 500;
-const HYBRID_KW_WEIGHT = 0.4;
-const HYBRID_SEM_WEIGHT = 0.6;
 const SEMANTIC_OVERFETCH = 3;
 const DEFAULT_BOOST_CAP = 2.0;
 function readBoostCap() {
@@ -79,10 +77,14 @@ export class FactRecallService {
             ...(input.kind !== undefined ? { kind: input.kind } : {}),
         };
         const candidates = await this.deps.factStore.listForRecall(filter);
-        if (candidates.length === 0)
-            return empty;
         const byId = new Map(candidates.map((f) => [f.id, f]));
         const queryTokens = queryText ? new Set(tokenSet(queryText)) : new Set();
+        // The keyword candidate set is recency-capped (listForRecall ORDER BY
+        // created_at DESC LIMIT STORAGE_FETCH_CAP). Semantic recall must reach the
+        // whole corpus, so it resolves vector neighbours independently of this
+        // window and re-applies the same filters via `accept`. Without this, ~93%
+        // of facts (everything older than the recent cap) were silently unreachable.
+        const accept = makeFilterPredicate(filter);
         const kwHits = mode === "keyword" || mode === "hybrid"
             ? scoreAll(candidates, queryTokens)
             : [];
@@ -90,7 +92,7 @@ export class FactRecallService {
         let semError = null;
         if ((mode === "semantic" || mode === "hybrid") && queryText) {
             try {
-                semHits = await this.runSemantic(queryText, byId, limit * SEMANTIC_OVERFETCH);
+                semHits = await this.runSemantic(queryText, byId, accept, limit * SEMANTIC_OVERFETCH);
             }
             catch (err) {
                 if (err instanceof LLMUnreachableError) {
@@ -126,7 +128,7 @@ export class FactRecallService {
             return finalize(queryText, subject, predicate, kind, mode, limit, boosted);
         }
         // hybrid
-        const merged = mergeHybrid(kwHits, semHits, byId);
+        const merged = mergeHybrid(kwHits, semHits);
         const boosted = await this.applyCorroboration(merged);
         const result = finalize(queryText, subject, predicate, kind, mode, limit, boosted);
         return semError ? { ...result, modeUnavailable: semError } : result;
@@ -182,19 +184,45 @@ export class FactRecallService {
             return hits;
         }
     }
-    async runSemantic(query, byId, fetchLimit) {
+    async runSemantic(query, byId, accept, fetchLimit) {
         const embedding = await this.deps.llm.embed(query, "query");
         const neighbors = await this.deps.factStore.semanticSearch(embedding.vector, fetchLimit);
+        // Resolve neighbours that fall outside the recency-capped keyword window
+        // in one batch, then apply the same filters the SQL pre-filter would have.
+        const missingIds = neighbors.filter((n) => !byId.has(n.factId)).map((n) => n.factId);
+        const fetched = missingIds.length > 0 ? await this.deps.factStore.getByIds(missingIds) : [];
+        const fetchedById = new Map(fetched.map((f) => [f.id, f]));
         const hits = [];
         for (const n of neighbors) {
-            const fact = byId.get(n.factId);
-            if (!fact)
-                continue; // candidate was filtered out by subject/predicate/conf
+            const fact = byId.get(n.factId) ?? fetchedById.get(n.factId);
+            if (!fact || !accept(fact))
+                continue;
             hits.push({ fact, similarity: cosineFromL2(n.distance) });
         }
         return hits;
     }
 }
+/**
+ * Replicates the SQL pre-filter (listForRecall) so semantic neighbours fetched
+ * outside the keyword candidate window are held to the same standard:
+ * non-superseded (unless requested), at/above the confidence floor, and
+ * matching any structured subject/predicate/kind constraint.
+ */
+function makeFilterPredicate(filter) {
+    return (f) => {
+        if (filter.includeSuperseded !== true && f.supersededBy !== null)
+            return false;
+        if (filter.minConfidence !== undefined && f.confidence < filter.minConfidence)
+            return false;
+        if (filter.kind !== undefined && f.kind !== filter.kind)
+            return false;
+        if (filter.subject !== undefined && f.subject !== filter.subject)
+            return false;
+        if (filter.predicate !== undefined && f.predicate !== filter.predicate)
+            return false;
+        return true;
+    };
+}
 function scoreAll(facts, queryTokens) {
     if (queryTokens.size === 0)
         return [];
@@ -227,30 +255,49 @@ function scoreFact(fact, queryTokens) {
     }
     return { score, matchedIn };
 }
-function mergeHybrid(kwHits, semHits, byId) {
-    const maxKw = Math.max(1, ...kwHits.map((h) => h.score));
+/**
+ * Semantic-primary hybrid merge.
+ *
+ * For short fact triples, semantic similarity is the dominant quality signal
+ * and the keyword leg is both recency-windowed (see listForRecall) and noisy
+ * (few tokens to match on). An equal-weight blend let high keyword scores on
+ * recent-but-wrong facts dilute strong semantic hits — measured ~14pts of R@5
+ * lost vs pure semantic on the paraphrase gold set (2026-06-16 report).
+ *
+ * So semantic hits occupy the upper score band [0.5, 1.0] (ranked by
+ * similarity); keyword-only hits — facts semantic never surfaced — backfill the
+ * lower band [0, 0.5). Co-occurrence isn't rewarded (that was the dilution
+ * source). When semantic is unavailable (Ollama down) semHits is empty and this
+ * degrades to pure keyword, preserving the graceful-degradation contract.
+ */
+function mergeHybrid(kwHits, semHits) {
     const maxSem = Math.max(1, ...semHits.map((h) => h.similarity));
+    const maxKw = Math.max(1, ...kwHits.map((h) => h.score));
     const kwMap = new Map(kwHits.map((h) => [h.fact.id, h]));
-    const semMap = new Map(semHits.map((h) => [h.fact.id, h]));
-    const allIds = new Set([...kwMap.keys(), ...semMap.keys()]);
     const rows = [];
-    for (const id of allIds) {
-        const fact = byId.get(id);
-        if (!fact)
-            continue;
-        const kw = kwMap.get(id);
-        const sem = semMap.get(id);
-        const kwNorm = kw ? kw.score / maxKw : 0;
-        const semNorm = sem ? sem.similarity / maxSem : 0;
-        const combined = round4(HYBRID_SEM_WEIGHT * semNorm + HYBRID_KW_WEIGHT * kwNorm);
-        const matchedIn = uniqueFields(kw?.matchedIn ?? [], sem ? ["semantic"] : []);
+    const seen = new Set();
+    for (const sem of semHits) {
+        const semNorm = sem.similarity / maxSem;
+        const kw = kwMap.get(sem.fact.id);
         rows.push({
-            ...fact,
-            matchScore: combined,
-            matchedIn,
-            keywordScore: round4(kwNorm),
+            ...sem.fact,
+            matchScore: round4(0.5 + 0.5 * semNorm),
+            matchedIn: uniqueFields(kw?.matchedIn ?? [], ["semantic"]),
+            keywordScore: round4(kw ? kw.score / maxKw : 0),
             semanticScore: round4(semNorm),
         });
+        seen.add(sem.fact.id);
+    }
+    for (const kw of kwHits) {
+        if (seen.has(kw.fact.id))
+            continue;
+        rows.push({
+            ...kw.fact,
+            matchScore: round4(0.5 * (kw.score / maxKw)),
+            matchedIn: kw.matchedIn,
+            keywordScore: round4(kw.score / maxKw),
+            semanticScore: 0,
+        });
     }
     rows.sort((a, b) => b.matchScore - a.matchScore);
     return rows;

package/dist/core/recall-facts/fact-recall-service.js.map

@@ -1 +1 @@
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package/dist/core/scheduler/scheduler.d.ts

@@ -21,8 +21,10 @@ import type { TranscriptAdapter } from "../../ports/transcript-adapter.js";
 import type { SignalStore } from "../../ports/signal-store.js";
 import type { SqliteFactStore } from "../storage/sqlite-fact-store.js";
 import type { SqliteSessionStore } from "../storage/sqlite-session-store.js";
+import { PgSessionStore } from "../storage/pg-session-store.js";
+import type { PgFactStore } from "../storage/pg-fact-store.js";
 export interface SchedulerOptions {
-    readonly store: SqliteSessionStore;
+    readonly store: SqliteSessionStore | PgSessionStore;
     readonly adapters: ReadonlyArray<TranscriptAdapter>;
     readonly classifier: LLMClient;
     readonly embedder?: LLMClient | null;
@@ -33,7 +35,7 @@ export interface SchedulerOptions {
      * with no facts written (backwards-compatible default for tests not yet
      * updated, and for any future caller that wants facts off).
      */
-    readonly factStore?: SqliteFactStore | null;
+    readonly factStore?: SqliteFactStore | PgFactStore | null;
     /** SignalStore for the self-improvement lane. When set, the tick drains
      *  each chunk's embedded nlm.signal payloads, decoupled from classification. */
     readonly signalStore?: SignalStore | null;

package/dist/core/scheduler/scheduler.js

@@ -21,6 +21,7 @@ import { dirname, join } from "node:path";
 import { homedir } from "node:os";
 import { extractFacts } from "../facts/extract-facts.js";
 import { normalizeSignal } from "../signals/ingest-signal.js";
+import { PgSessionStore } from "../storage/pg-session-store.js";
 import { MAX_CLASSIFY_FAILURES, getFileSize, recordClassified, recordClassifiedPg, recordFailed, recordFailedPg, recordSkippedLowConfidence, recordSkippedLowConfidencePg, scanOnce, scanOncePg } from "./scan-once.js";
 import { runCheapChecksOnSqlite } from "../integrity/check-invariants.js";
 const DEFAULT_INTERVAL_MS = 30 * 60 * 1000; // 30 min, matches Python default
@@ -102,10 +103,14 @@ export class ScanScheduler {
         let storageFailures = 0;
         let chunksSeen = 0;
         const now = Date.now();
-        const _pgPool = this.opts.store.pgPool?.();
+        // Backend split: exactly one of (_pgPool, sqliteDb) is non-null. PG branches
+        // use the pool; SQLite branches use the raw better-sqlite3 handle.
+        const store = this.opts.store;
+        const _pgPool = store instanceof PgSessionStore ? store.pool : null;
+        const sqliteDb = store instanceof PgSessionStore ? null : store.rawDb();
         if (!_pgPool && shouldRunIntegrityCheck(now)) {
             try {
-                const violations = runCheapChecksOnSqlite(this.opts.store.rawDb());
+                const violations = runCheapChecksOnSqlite(sqliteDb);
                 markIntegrityCheckRan(now);
                 for (const v of violations) {
                     this.opts.logger(`[integrity] FAIL ${v.id} count=${v.count} ${v.description}  run \`nlm doctor\` to inspect or \`nlm doctor --fix\` to repair`);
@@ -120,7 +125,7 @@ export class ScanScheduler {
             try {
                 results = _pgPool
                     ? await scanOncePg(adapter, this.opts.idleMinutes, _pgPool)
-                    : await scanOnce(adapter, this.opts.idleMinutes, this.opts.store.rawDb());
+                    : await scanOnce(adapter, this.opts.idleMinutes, sqliteDb);
             }
             catch (e) {
                 this.opts.logger(`[scheduler] scanOnce error for ${adapter.name}: ${e instanceof Error ? e.message : String(e)}`);
@@ -141,8 +146,8 @@ export class ScanScheduler {
                         count = await recordFailedPg(_pgPool, adapter.name, chunk.sourcePath, getFileSize(chunk.sourcePath));
                     }
                     else {
-                        recordFailed(this.opts.store.rawDb(), adapter.name, chunk.sourcePath);
-                        count = this.opts.store.rawDb()
+                        recordFailed(sqliteDb, adapter.name, chunk.sourcePath);
+                        count = sqliteDb
                             .prepare("SELECT COALESCE(failure_count, 0) AS failure_count FROM adapter_state WHERE adapter_name = ? AND source_path = ?")
                             .get(adapter.name, chunk.sourcePath)?.failure_count ?? 1;
                     }
@@ -156,7 +161,7 @@ export class ScanScheduler {
                         await recordSkippedLowConfidencePg(_pgPool, adapter.name, chunk.sourcePath);
                     }
                     else {
-                        recordSkippedLowConfidence(this.opts.store.rawDb(), adapter.name, chunk.sourcePath);
+                        recordSkippedLowConfidence(sqliteDb, adapter.name, chunk.sourcePath);
                     }
                     this.opts.logger(`[scheduler] low-confidence (${classification.confidence} < ${this.opts.confidenceFloor}) for ${chunk.id} - skipping until file grows`);
                     continue;
@@ -180,19 +185,25 @@ export class ScanScheduler {
                     decisions: classification.decisions,
                     openQuestions: classification.open,
                 };
-                const factSink = this.opts.factStore
-                    ? {
-                        factStore: this.opts.factStore,
-                        facts: extractFacts(classification, chunk.id, chunk.startedAt),
-                    }
-                    : null;
+                const supersedesArg = supersedes ? { priorSessionId: supersedes, kind: "replaces" } : null;
+                const facts = this.opts.factStore
+                    ? extractFacts(classification, chunk.id, chunk.startedAt)
+                    : [];
                 try {
-                    await this.opts.store.insertSession(record, this.opts.embedder, supersedes ? { priorSessionId: supersedes, kind: "replaces" } : null, factSink);
+                    // Store + factStore are constructed from the same backend, so the
+                    // factStore cast below is sound — TS just can't correlate the two
+                    // union members across a single call site.
+                    if (store instanceof PgSessionStore) {
+                        await store.insertSession(record, this.opts.embedder, supersedesArg, this.opts.factStore ? { factStore: this.opts.factStore, facts } : null);
+                    }
+                    else {
+                        await store.insertSession(record, this.opts.embedder, supersedesArg, this.opts.factStore ? { factStore: this.opts.factStore, facts } : null);
+                    }
                     if (_pgPool) {
                         await recordClassifiedPg(_pgPool, adapter.name, chunk.sourcePath, chunk.id);
                     }
                     else {
-                        recordClassified(this.opts.store.rawDb(), adapter.name, chunk.sourcePath, chunk.id);
+                        recordClassified(sqliteDb, adapter.name, chunk.sourcePath, chunk.id);
                     }
                     inserted += 1;
                 }
@@ -202,7 +213,7 @@ export class ScanScheduler {
                         await recordFailedPg(_pgPool, adapter.name, chunk.sourcePath, getFileSize(chunk.sourcePath));
                     }
                     else {
-                        recordFailed(this.opts.store.rawDb(), adapter.name, chunk.sourcePath);
+                        recordFailed(sqliteDb, adapter.name, chunk.sourcePath);
                     }
                     this.opts.logger(`[scheduler] storage error for ${chunk.id}: ${e instanceof Error ? e.message : String(e)}`);
                 }