nlm-memory 0.21.0 → 0.21.13

package/dist/core/dataset/build-dataset.js

@@ -6,6 +6,21 @@
  * alerts, snoozed entities, retired labels, merged variants) are deferred:
  * the action log isn't yet exposed by the TS daemon. Returns persisted
  * state directly.
+ *
+ * Tenancy (program spec §4.6 hardening 1, M2 plan Wave B6): `buildDataset`
+ * takes `tenantId` and constrains every table read — direct WHERE via
+ * `tenantClause` for the STAMP tables (`sessions`, `entities`), a join back
+ * to the tenant-filtered session id set for the DERIVE tables
+ * (`session_entities`, `markers`, `session_edges`), and the same
+ * subject-resolvability predicate as `actions-log.ts` for the action
+ * overlay — even though the `GET /api/dataset` route itself is
+ * LOCAL-dispositioned and 403s in hosted mode (Wave C's hosted-mode gate).
+ * This is defense-in-depth: the guard test scans this file's SQL
+ * regardless of the route's gate, and a future caller that reuses this
+ * function outside the gated route stays safe by construction.
+ * `computeIntegrityAlerts` (below) is the one exception, documented at its
+ * call site — it stays whole-DB, matching the `sqliteDataStats` treatment
+ * of migration/structural bookkeeping.
  */
 import { existsSync } from "node:fs";
 import Database from "better-sqlite3";
@@ -13,6 +28,7 @@ import * as sqliteVec from "sqlite-vec";
 import { liveSessionStatus } from "../storage/live-status.js";
 import { loadActionOverlay, openQuestionId, decisionId } from "../actions/overlay.js";
 import { runCheapChecksOnSqlite } from "../integrity/check-invariants.js";
+import { tenantClause } from "../tenancy/tenant-clause.js";
 const EMPTY_DATASET = (dbPath, present) => ({
     meta: {
         last_sync: new Date().toISOString(),
@@ -31,7 +47,7 @@ const EMPTY_DATASET = (dbPath, present) => ({
     alerts: [],
     runtimes: [],
 });
-export function buildDataset(dbPath, options = {}) {
+export function buildDataset(dbPath, tenantId, options = {}) {
     if (!existsSync(dbPath))
         return EMPTY_DATASET(dbPath, false);
     const db = new Database(dbPath, { readonly: true });
@@ -42,7 +58,7 @@ export function buildDataset(dbPath, options = {}) {
         // vec extension only required for semantic search; tolerable here.
     }
     try {
-        return projectFromDb(db, dbPath, options.includePaths ?? false);
+        return projectFromDb(db, dbPath, tenantId, options.includePaths ?? false);
     }
     finally {
         db.close();
@@ -69,46 +85,79 @@ export function isPathShapedEntity(canonical) {
         return true;
     return false;
 }
-function projectFromDb(db, dbPath, includePaths) {
+/**
+ * Split an id list into chunks that fit SQLite's bound-variable cap
+ * (SQLITE_LIMIT_VARIABLE_NUMBER, 32,766 in the bundled better-sqlite3).
+ * Sized so even double-bound IN queries (session_edges binds the chunk
+ * twice) stay under the cap.
+ */
+const IN_QUERY_CHUNK_SIZE = 400;
+function chunkIds(ids) {
+    const chunks = [];
+    for (let i = 0; i < ids.length; i += IN_QUERY_CHUNK_SIZE) {
+        chunks.push(ids.slice(i, i + IN_QUERY_CHUNK_SIZE));
+    }
+    return chunks;
+}
+function projectFromDb(db, dbPath, tenantId, includePaths) {
+    const sessionsTc = tenantClause(tenantId);
     const sessionRows = db
         .prepare(`
       SELECT id, started_at, ended_at, duration_min, label, summary,
              status, transcript_path, runtime
       FROM sessions
+      WHERE ${sessionsTc.sql}
       ORDER BY started_at ASC
     `)
-        .all();
+        .all(sessionsTc.param);
     if (sessionRows.length === 0)
         return EMPTY_DATASET(dbPath, true);
+    // session_entities/markers/session_edges carry no tenant_id (DERIVE) — ids
+    // are already sourced from the tenant-filtered sessions query above, so a
+    // plain IN is sufficient (mirrors SqliteSessionStore.loadMarkers/
+    // loadSessionEdges, which take an already tenant-resolved id list).
+    //
+    // Chunked: SQLite caps a statement at 32,766 bound variables
+    // (SQLITE_LIMIT_VARIABLE_NUMBER in the bundled better-sqlite3), and these
+    // id lists grow with the corpus — past it, GET /api/dataset 500s with
+    // "too many SQL variables" (2026-10-01, 18,868 sessions). The edges query
+    // binds the chunk twice, so the chunk size stays far under half the cap.
+    const sessionIds = sessionRows.map((s) => s.id);
     const entitiesBySession = new Map();
-    for (const r of db
-        .prepare("SELECT session_id, entity_canonical FROM session_entities ORDER BY session_id")
-        .all()) {
-        const list = entitiesBySession.get(r.session_id);
-        if (list)
-            list.push(r.entity_canonical);
-        else
-            entitiesBySession.set(r.session_id, [r.entity_canonical]);
-    }
-    const decisionsBySession = new Map();
-    const openBySession = new Map();
-    for (const r of db
-        .prepare("SELECT session_id, kind, text, position FROM markers ORDER BY session_id, position")
-        .all()) {
-        if (r.kind === "decision") {
-            const list = decisionsBySession.get(r.session_id);
+    for (const idChunk of chunkIds(sessionIds)) {
+        const placeholders = idChunk.map(() => "?").join(",");
+        for (const r of db
+            .prepare(`SELECT session_id, entity_canonical FROM session_entities WHERE session_id IN (${placeholders}) ORDER BY session_id`)
+            .all(...idChunk)) {
+            const list = entitiesBySession.get(r.session_id);
             if (list)
-                list.push(r.text);
+                list.push(r.entity_canonical);
             else
-                decisionsBySession.set(r.session_id, [r.text]);
+                entitiesBySession.set(r.session_id, [r.entity_canonical]);
         }
-        else {
-            const id = openQuestionId(r.session_id, r.text);
-            const list = openBySession.get(r.session_id);
-            if (list)
-                list.push({ id, text: r.text });
-            else
-                openBySession.set(r.session_id, [{ id, text: r.text }]);
+    }
+    const decisionsBySession = new Map();
+    const openBySession = new Map();
+    for (const idChunk of chunkIds(sessionIds)) {
+        const placeholders = idChunk.map(() => "?").join(",");
+        for (const r of db
+            .prepare(`SELECT session_id, kind, text, position FROM markers WHERE session_id IN (${placeholders}) ORDER BY session_id, position`)
+            .all(...idChunk)) {
+            if (r.kind === "decision") {
+                const list = decisionsBySession.get(r.session_id);
+                if (list)
+                    list.push(r.text);
+                else
+                    decisionsBySession.set(r.session_id, [r.text]);
+            }
+            else {
+                const id = openQuestionId(r.session_id, r.text);
+                const list = openBySession.get(r.session_id);
+                if (list)
+                    list.push({ id, text: r.text });
+                else
+                    openBySession.set(r.session_id, [{ id, text: r.text }]);
+            }
         }
     }
     const supersedesBy = new Map();
@@ -116,28 +165,33 @@ function projectFromDb(db, dbPath, includePaths) {
     const replacesBy = new Map();
     const replacedByBy = new Map();
     const continuesBy = new Map();
-    for (const r of db
-        .prepare("SELECT from_session, to_session, kind FROM session_edges")
-        .all()) {
-        if (r.kind === "supersedes") {
-            supersedesBy.set(r.from_session, r.to_session);
-            supersededByBy.set(r.to_session, r.from_session);
-        }
-        else if (r.kind === "replaces") {
-            replacesBy.set(r.from_session, r.to_session);
-            replacedByBy.set(r.to_session, r.from_session);
-        }
-        else if (r.kind === "continues") {
-            continuesBy.set(r.from_session, r.to_session);
+    for (const idChunk of chunkIds(sessionIds)) {
+        const placeholders = idChunk.map(() => "?").join(",");
+        for (const r of db
+            .prepare(`SELECT from_session, to_session, kind FROM session_edges
+         WHERE from_session IN (${placeholders}) OR to_session IN (${placeholders})`)
+            .all(...idChunk, ...idChunk)) {
+            if (r.kind === "supersedes") {
+                supersedesBy.set(r.from_session, r.to_session);
+                supersededByBy.set(r.to_session, r.from_session);
+            }
+            else if (r.kind === "replaces") {
+                replacesBy.set(r.from_session, r.to_session);
+                replacedByBy.set(r.to_session, r.from_session);
+            }
+            else if (r.kind === "continues") {
+                continuesBy.set(r.from_session, r.to_session);
+            }
         }
     }
+    const entitiesTc = tenantClause(tenantId);
     const allEntityRows = db
         .prepare(`
       SELECT canonical, type, status, session_count, last_seen_session
-      FROM entities ORDER BY session_count DESC
+      FROM entities WHERE ${entitiesTc.sql} ORDER BY session_count DESC
     `)
-        .all();
-    const overlay = loadActionOverlay(db);
+        .all(entitiesTc.param);
+    const overlay = loadActionOverlay(db, tenantId);
     // Count-folding pass (Option B): runs before coherence computation so the
     // target entity's bucket reflects the absorbed session count.
     if (overlay.mergedEntities.size > 0) {
@@ -235,6 +289,12 @@ function projectFromDb(db, dbPath, includePaths) {
     }
     const metrics = computeMetrics(sessions, entityRows);
     const staleAlerts = computeStaleAlerts(sessions, entityRows, overlay);
+    // Whole-DB by design, not tenant-constrained: these are schema/referential
+    // integrity checks (orphaned edges, cyclic supersedence, ghost embedding
+    // rows), not corpus content — the same class of migration/structural
+    // bookkeeping sqliteDataStats leaves whole-DB. Tenant-scoping would give a
+    // false sense of per-tenant isolation for a check whose whole point is
+    // spotting corruption that isn't supposed to respect any boundary.
     const integrityAlerts = computeIntegrityAlerts(db);
     const alerts = [...staleAlerts, ...integrityAlerts];
     const runtimes = computeRuntimes(sessions);

package/dist/core/dataset/build-dataset.js.map

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package/dist/core/digest/compose.d.ts

@@ -11,6 +11,7 @@
  * push. Probe/test queries are filtered out of both windows.
  */
 import type { OutcomeCoverage } from "../outcome/coverage.js";
+import type { JobSnapshot } from "../jobs/job-supervisor.js";
 export interface RecallStats {
     readonly total: number;
     readonly hit_rate: number;
@@ -41,6 +42,13 @@ export interface ComposeInput {
     readonly precision?: DigestPrecision | null;
     /** Tier-B outcome rollup over sessions ended in the last 30 days (#352 phase 2). */
     readonly outcomeCoverage?: OutcomeCoverage | null;
+    /**
+     * JobSupervisor's reprocess snapshot (#414). Null/absent covers both "never
+     * started" and "daemon restarted mid-run" — the supervisor holds no
+     * persisted state across restarts, so a fresh process reports `idle` the
+     * same as one that never ran, and that's rendered as "no active job".
+     */
+    readonly job?: JobSnapshot | null;
     /** Override "now" for deterministic tests; defaults to Date.now(). */
     readonly now?: Date;
 }

package/dist/core/digest/compose.js

@@ -55,6 +55,7 @@ export function composeDigest(input) {
         `Last 7d: ${real7d} real / ${total7d} total · surfaced ${pct(input.stats.hit_rate)}\n` +
         `Recall precision (cited/surfaced): ${formatPrecision(input.precision)}\n` +
         `${formatOutcomeCoverage(input.outcomeCoverage)}\n` +
+        `${formatJobLine(input.job, now)}\n` +
         `\n` +
         `Top real queries (24h):\n` +
         `${topLines}\n` +
@@ -77,6 +78,59 @@ function formatOutcomeCoverage(c) {
         `held ${share(c.held)} · overturned ${share(c.overturned)} · built-upon ${share(c.builtUpon)} · ` +
         `re-derived ${share(c.reDerivedLater)} · unobserved ${share(c.unobserved)}`);
 }
+/**
+ * One-line reprocess status for the digest. `idle` and the null/absent case
+ * render identically ("no active job") — see the `job` field doc above for
+ * why a daemon restart mid-run collapses to the same line as never-started.
+ */
+function formatJobLine(job, now) {
+    if (!job)
+        return "Jobs: no active job";
+    const { name, processed, total, restarts, restartsTotal, lastAdvanceAt } = job;
+    switch (job.state) {
+        case "running": {
+            const advance = lastAdvanceAt ? `last advance ${formatAgo(lastAdvanceAt, now)}` : "no progress yet";
+            // restartsTotal is the lifetime respawn count for this run (never
+            // reset by progress, unlike `restarts`) — surfaced only when >0 so an
+            // OOM-churning run that keeps making progress between crashes isn't
+            // silently indistinguishable from a clean one.
+            const restartSuffix = restartsTotal > 0 ? `, ${restartsTotal} restart${restartsTotal === 1 ? "" : "s"}` : "";
+            return `Jobs: ${name} ${processed}/${total}, ${advance}${restartSuffix}`;
+        }
+        case "stalled": {
+            const advance = lastAdvanceAt ? `last advance ${formatAgo(lastAdvanceAt, now)}` : "no progress yet";
+            return `Jobs: ${name} stalled at ${processed}/${total}, ${advance}`;
+        }
+        case "completed":
+            return `Jobs: ${name} completed ${processed}/${total}`;
+        case "exhausted":
+            // `restarts` at exhaustion already counts the refused final attempt
+            // (see job-alert.ts's buildJobAlertEvent) — "fruitless" frames the
+            // count as restarts that led nowhere, not restarts still to come.
+            return (`Jobs: ${name} gave up after ${restarts} fruitless restart${restarts === 1 ? "" : "s"} ` +
+                `(${processed}/${total} processed)`);
+        case "stopped":
+            return `Jobs: ${name} stopped at ${processed}/${total}`;
+        case "idle":
+        default:
+            return "Jobs: no active job";
+    }
+}
+function formatAgo(iso, now) {
+    const t = Date.parse(iso);
+    if (!Number.isFinite(t))
+        return "unknown";
+    const s = Math.max(0, Math.floor((now.getTime() - t) / 1000));
+    if (s < 60)
+        return `${s}s ago`;
+    const m = Math.floor(s / 60);
+    if (m < 60)
+        return `${m}m ago`;
+    const h = Math.floor(m / 60);
+    if (h < 24)
+        return `${h}h ago`;
+    return `${Math.floor(h / 24)}d ago`;
+}
 function truncate(s, max) {
     if (s.length <= max)
         return s;

package/dist/core/digest/compose.js.map

@@ -1 +1 @@
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package/dist/core/digest/hook-injection.d.ts

@@ -40,4 +40,4 @@ export interface InjectionCheckResult {
  *
  * Pure function: no I/O, no side effects. Pass the raw hook-log lines.
  */
-export declare function checkHookInjection(entries: ReadonlyArray<InjectionLogEntry>, now?: Date): InjectionCheckResult;
+export declare function checkHookInjection(entries: ReadonlyArray<InjectionLogEntry>, now?: Date, ambientRecallEnabled?: boolean): InjectionCheckResult;

package/dist/core/digest/hook-injection.js

@@ -29,7 +29,15 @@ const MIN_FIRES = 10;
  *
  * Pure function: no I/O, no side effects. Pass the raw hook-log lines.
  */
-export function checkHookInjection(entries, now) {
+export function checkHookInjection(entries, now, ambientRecallEnabled = true) {
+    // Option B (NLM_HOOK_PROMPT_RECALL=off) disables ambient per-prompt
+    // injection outright, so every fire logs hits: [] / wouldInject: [] by
+    // design — the same reason the gate === "generative" | "skip" fires are
+    // skipped below, applied at the feature level instead of the prompt level.
+    // Without this the canary warns every single morning about a lane the
+    // operator deliberately turned off, which trains them to ignore the digest.
+    if (!ambientRecallEnabled)
+        return { ok: true, message: null };
     const cutoff = (now ?? new Date()).getTime() - WINDOW_MS;
     let fires = 0;
     let injecting = 0;

package/dist/core/digest/hook-injection.js.map

@@ -1 +1 @@
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package/dist/core/digest/hook-version-parity.d.ts

@@ -0,0 +1,31 @@
+/**
+ * Hook version parity — companion to the hook-liveness canary.
+ *
+ * hook-liveness.ts answers "did hooks fire?". It structurally cannot answer
+ * "did the RIGHT hooks fire?", so a hook executing stale code out of some other
+ * install passes it cleanly. On 2026-08-14 that gap hid a real regression for
+ * nine days: the five Claude Code hooks ran a 0.21.0 build from a dev checkout
+ * while the daemon served 0.21.3, and every existing check stayed green,
+ * because firing and being-current are different properties.
+ *
+ * Hooks stamp their own version into each hook-log entry (`v`). This compares
+ * the most recent LIVE fire against the version the daemon/CLI expects.
+ *
+ * Reading only the newest live fire is deliberate. Scanning a window would
+ * keep alerting for a day after every legitimate upgrade, because the window
+ * still contains pre-upgrade entries — and an alert that cries wolf after
+ * routine upgrades gets muted, which is how the original drift survived. The
+ * newest fire self-clears the moment an upgraded hook runs once, while a hook
+ * that really is stale keeps reporting the old version indefinitely.
+ *
+ * A newest fire with no `v` at all is treated as a mismatch, not as missing
+ * data: hooks that predate the stamp are, by definition, the stale build this
+ * check exists to catch.
+ */
+export interface VersionedHookLogEntry {
+    readonly ts?: string;
+    readonly mode?: string;
+    /** Hook's own version, stamped at write time. Absent on pre-stamp builds. */
+    readonly v?: string;
+}
+export declare function checkHookVersionParity(hookLog: ReadonlyArray<VersionedHookLogEntry>, expectedVersion: string | undefined): string | null;

package/dist/core/digest/hook-version-parity.js

@@ -0,0 +1,56 @@
+/**
+ * Hook version parity — companion to the hook-liveness canary.
+ *
+ * hook-liveness.ts answers "did hooks fire?". It structurally cannot answer
+ * "did the RIGHT hooks fire?", so a hook executing stale code out of some other
+ * install passes it cleanly. On 2026-08-14 that gap hid a real regression for
+ * nine days: the five Claude Code hooks ran a 0.21.0 build from a dev checkout
+ * while the daemon served 0.21.3, and every existing check stayed green,
+ * because firing and being-current are different properties.
+ *
+ * Hooks stamp their own version into each hook-log entry (`v`). This compares
+ * the most recent LIVE fire against the version the daemon/CLI expects.
+ *
+ * Reading only the newest live fire is deliberate. Scanning a window would
+ * keep alerting for a day after every legitimate upgrade, because the window
+ * still contains pre-upgrade entries — and an alert that cries wolf after
+ * routine upgrades gets muted, which is how the original drift survived. The
+ * newest fire self-clears the moment an upgraded hook runs once, while a hook
+ * that really is stale keeps reporting the old version indefinitely.
+ *
+ * A newest fire with no `v` at all is treated as a mismatch, not as missing
+ * data: hooks that predate the stamp are, by definition, the stale build this
+ * check exists to catch.
+ */
+export function checkHookVersionParity(hookLog, expectedVersion) {
+    if (!expectedVersion)
+        return null;
+    let newest = null;
+    let newestTs = -Infinity;
+    for (const entry of hookLog) {
+        if (entry.mode !== "live")
+            continue;
+        const ts = entry.ts ? Date.parse(entry.ts) : NaN;
+        if (!Number.isFinite(ts))
+            continue;
+        if (ts > newestTs) {
+            newestTs = ts;
+            newest = entry;
+        }
+    }
+    // No live fires at all is liveness's alert to raise, not this one.
+    if (!newest)
+        return null;
+    if (!newest.v) {
+        return (`WARN hook version unknown: the most recent live hook fire reports no ` +
+            `version, so it predates the parity stamp and is running an older build ` +
+            `than ${expectedVersion} — check the hook commands in ~/.claude/settings.json`);
+    }
+    if (newest.v !== expectedVersion) {
+        return (`WARN hook version skew: hooks are running ${newest.v} but the install is ` +
+            `${expectedVersion} — the hook commands in ~/.claude/settings.json point at ` +
+            `a different build than the daemon`);
+    }
+    return null;
+}
+//# sourceMappingURL=hook-version-parity.js.map

package/dist/core/digest/hook-version-parity.js.map

@@ -0,0 +1 @@
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package/dist/core/embedding/pg-embed-backfill.js

@@ -46,7 +46,7 @@ export async function reembedCorpusPg(opts) {
     const statePath = opts.statePath ?? DEFAULT_STATE_PATH;
     const pool = new Pool({ connectionString: opts.pgUrl });
     try {
-        const tableCheck = await pool.query("SELECT EXISTS (SELECT 1 FROM information_schema.tables WHERE table_schema = 'public' AND table_name = 'embedding_config') AS exists");
+        const tableCheck = await pool.query("SELECT EXISTS (SELECT 1 FROM information_schema.tables WHERE table_schema = current_schema() AND table_name = 'embedding_config') AS exists");
         if (!tableCheck.rows[0]?.exists) {
             throw new Error("embedding_config table not found; run `nlm migrate` to apply pending migrations");
         }

package/dist/core/embedding/pg-embed-backfill.js.map

@@ -1 +1 @@
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package/dist/core/exemplars/capture-from-session.d.ts

@@ -32,4 +32,4 @@ export interface DrainExemplarDeps {
     readonly codeEmbedder?: CodeEmbedder | null;
     readonly logger?: (msg: string) => void;
 }
-export declare function drainSessionExemplars(ctx: SessionExemplarContext, deps: DrainExemplarDeps): Promise<number>;
+export declare function drainSessionExemplars(tenantId: string, ctx: SessionExemplarContext, deps: DrainExemplarDeps): Promise<number>;