test(dream): conform dream-dir-source-stamp to canonical PGLite isolation pattern

check:test-isolation R3/R4 flagged the new test file: engine was created
in beforeEach (outside beforeAll) and never disconnected in afterAll.
Switch to the canonical shared-engine pattern (beforeAll create,
beforeEach resetPgliteState, afterAll disconnect) per
test/helpers/reset-pglite.ts.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/commands/autopilot.ts

@@ -38,6 +38,7 @@ import { logSelfUpgrade } from '../core/audit/self-upgrade-audit.ts';
 import { detectInstallMethod } from './upgrade.ts';
 import { evaluateQuietHours } from '../core/minions/quiet-hours.ts';
 import { inspectLock } from '../core/db-lock.ts';
+import { registerCleanup } from '../core/process-cleanup.ts';
 
 /**
  * v0.37.7.0 #1162 — classify autopilot reconnect-loop errors.
@@ -433,6 +434,37 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
   let stopping = false;
   let childSupervisor: ChildWorkerSupervisor | null = null;
 
+  // #1872: graceful engine shutdown. On PGLite the cycle steps run INLINE in
+  // this process, so a hard `process.exit` mid-write (systemctl stop →
+  // SIGTERM) kills WASM Postgres with the WAL dirty and can corrupt the
+  // brain. Two exit paths must both close the engine:
+  //   - autopilot's own shutdown() below (owns SIGINT + internal stops like
+  //     max_crashes / cycle-failure-cap), and
+  //   - process-cleanup's SIGTERM handler (installed at cli.ts module load;
+  //     it runs the cleanup registry with a 3s deadline and then exits) —
+  //     which is why closeEngine is ALSO registered there.
+  // closeEngine aborts the in-flight inline cycle (runCycle checks the
+  // signal between phases and threads it into phase sub-work), gives it a
+  // short bounded window to wind down, then disconnects. PGLite's
+  // disconnect() drains the pending query and checkpoints before closing;
+  // a second call is a no-op (disconnect snapshots + nulls the handle), so
+  // both paths firing is safe.
+  const shutdownAbort = new AbortController();
+  let inflightInlineCycle: Promise<unknown> | null = null;
+  const closeEngine = async () => {
+    shutdownAbort.abort(new Error('autopilot shutdown'));
+    if (inflightInlineCycle) {
+      // ponytail: 2s cap keeps us inside process-cleanup's 3s deadline; a
+      // between-phase abort resolves instantly, a mid-phase one may not.
+      await Promise.race([
+        inflightInlineCycle.catch(() => { /* cycle errors already logged by the loop */ }),
+        new Promise((r) => setTimeout(r, 2_000)),
+      ]);
+    }
+    try { await engine.disconnect(); } catch { /* best-effort */ }
+  };
+  const deregisterEngineClose = registerCleanup('autopilot-engine-close', closeEngine);
+
   if (spawnManagedWorker) {
     const cliPath = resolveGbrainCliPath();
     // Cgroup-aware auto-sized RSS watchdog cap (issue #1678). The old flat
@@ -520,6 +552,10 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         childSupervisor.killChild('SIGKILL');
       }
     }
+    // #1872: abort the in-flight inline cycle and close the engine BEFORE
+    // process.exit — a hard exit mid-write corrupts PGLite's WASM Postgres.
+    await closeEngine();
+    deregisterEngineClose();
     try { unlinkSync(lockPath); } catch { /* already gone */ }
     process.exit(0);
   };
@@ -1008,16 +1044,21 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       // path's phase set). Now both converge on the same primitive.
       try {
         const { runCycle } = await import('../core/cycle.ts');
-        const report = await runCycle(engine, {
+        // #1872: track the promise so closeEngine can drain it on shutdown,
+        // and pass the abort signal so the cycle winds down between phases.
+        const cyclePromise = runCycle(engine, {
           brainDir: repoPath,
           // Autopilot daemon path: pulls by default (matches
           // pre-v0.17 autopilot behavior). CLI dream defaults false
           // for cron safety; that choice is scoped to dream only.
           pull: true,
+          signal: shutdownAbort.signal,
           yieldBetweenPhases: async () => {
             await new Promise(r => setImmediate(r));
           },
         });
+        inflightInlineCycle = cyclePromise;
+        const report = await cyclePromise.finally(() => { inflightInlineCycle = null; });
         // Only 'failed' (every attempted phase failed) trips the autopilot
         // circuit breaker. 'partial' means at least one phase warned or
         // failed while others ran — that's a soft signal, not a fatal

src/commands/dream.ts

@@ -26,6 +26,7 @@
 import type { BrainEngine } from '../core/engine.ts';
 import {
   runCycle,
+  resolveSourceForDir,
   ALL_PHASES,
   type CyclePhase,
   type CycleReport,
@@ -380,9 +381,9 @@ Options:
 
   --source <id>       Scope the cycle to one source so doctor's
                       cycle_freshness check sees a fresh stamp on
-                      completion. Without this, gbrain dream's
-                      timestamp never lands and federated brains
-                      see "stale cycle" forever.
+                      completion. When omitted, gbrain derives the
+                      source from --dir / the configured checkout
+                      when it matches a source's local_path (#1869).
   --source-id <id>    Alias for --source. Matches the v0.37.7.0+
                       naming used by import/extract/graph-query.
 
@@ -634,6 +635,25 @@ export async function runDream(engine: BrainEngine | null, args: string[]): Prom
     );
     process.exit(1);
   }
+
+  // #1869: a path-scoped run (--dir, or the configured sync.repo_path) whose
+  // directory matches a registered source's local_path IS that source's cycle
+  // — derive the source id so runCycle writes last_source_cycle_at /
+  // last_full_cycle_at on success and doctor's cycle_freshness check stops
+  // reading perpetually stale. Explicit --source still wins (resolved above).
+  // Fixed here at the command level, NOT in runCycle's stamp gate, so legacy
+  // global callers (autopilot-global-maintenance runs GLOBAL_PHASES with a
+  // brainDir and no sourceId) can't falsely stamp per-source freshness.
+  // A derived match on an archived source is skipped silently (falls back to
+  // legacy unscoped behavior) — stamping it would mask staleness on restore,
+  // mirroring the explicit --source archived guard above.
+  if (resolvedSourceId === undefined && engine !== null && brainDir !== null) {
+    const derived = await resolveSourceForDir(engine, brainDir);
+    if (derived !== undefined) {
+      const src = await fetchSource(engine, derived);
+      if (src?.archived !== true) resolvedSourceId = derived;
+    }
+  }
   // ─── issue #1678: bounded single-hold extract_atoms drain ──────────
   if (opts.drain) {
     if (engine === null) {

src/commands/embed.ts

@@ -1,5 +1,5 @@
 import type { BrainEngine } from '../core/engine.ts';
-import { embedBatch, currentEmbeddingSignature, resolveEmbeddingModelLabel } from '../core/embedding.ts';
+import { embedBatch, currentEmbeddingSignature } from '../core/embedding.ts';
 import type { ChunkInput } from '../core/types.ts';
 import { chunkText } from '../core/chunkers/recursive.ts';
 import { createProgress, type ProgressReporter } from '../core/progress.ts';
@@ -581,16 +581,11 @@ async function embedPage(
   for (let j = 0; j < toEmbed.length; j++) {
     embeddingMap.set(toEmbed[j].chunk_index, embeddings[j]);
   }
-  // #1717: label each (re)embedded chunk with the model that actually
-  // produced its vector. Preserved chunks (not re-embedded this pass) keep
-  // their existing model so a mixed-model page isn't relabeled wholesale.
-  const embedModelLabel = resolveEmbeddingModelLabel();
   const updated: ChunkInput[] = chunks.map(c => ({
     chunk_index: c.chunk_index,
     chunk_text: c.chunk_text,
     chunk_source: c.chunk_source,
     embedding: embeddingMap.get(c.chunk_index),
-    model: embeddingMap.has(c.chunk_index) && embedModelLabel ? embedModelLabel : c.model,
     token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
   }));
 
@@ -722,16 +717,12 @@ async function embedAll(
       for (let j = 0; j < toEmbed.length; j++) {
         embeddingMap.set(toEmbed[j].chunk_index, embeddings[j]);
       }
-      // #1717: stamp the resolved embedding model on (re)embedded chunks;
-      // preserve the existing model on chunks left untouched.
-      const embedModelLabel = resolveEmbeddingModelLabel();
       // Preserve ALL chunks, only update embeddings for stale ones
       const updated: ChunkInput[] = chunks.map(c => ({
         chunk_index: c.chunk_index,
         chunk_text: c.chunk_text,
         chunk_source: c.chunk_source,
         embedding: embeddingMap.get(c.chunk_index) ?? undefined,
-        model: embeddingMap.has(c.chunk_index) && embedModelLabel ? embedModelLabel : c.model,
         token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
       }));
       await observed(pacer, () => engine.upsertChunks(page.slug, updated, pageOpts));
@@ -1021,15 +1012,11 @@ async function embedAllStale(
           for (let j = 0; j < stale.length; j++) {
             staleIdxToEmbedding.set(stale[j].chunk_index, embeddings[j]);
           }
-          // #1717: label the re-embedded (stale) chunks with the resolved
-          // model; preserve the existing model on the non-stale chunks.
-          const embedModelLabel = resolveEmbeddingModelLabel();
           const merged: ChunkInput[] = existing.map(c => ({
             chunk_index: c.chunk_index,
             chunk_text: c.chunk_text,
             chunk_source: c.chunk_source,
             embedding: staleIdxToEmbedding.get(c.chunk_index) ?? undefined,
-            model: staleIdxToEmbedding.has(c.chunk_index) && embedModelLabel ? embedModelLabel : c.model,
             token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
           }));
           await observed(pacer, () => engine.upsertChunks(slug, merged, { sourceId: keySourceId }));

src/core/cycle.ts

@@ -855,8 +855,16 @@ interface SyncPhaseResult extends PhaseResult {
  * Resolve the source id for a brain directory by looking up the sources
  * table. Returns undefined when no registered source matches (falls back
  * to pre-v0.18 global config.sync.* keys).
+ *
+ * Exported for dream.ts (#1869): a `gbrain dream --dir <path>` run whose
+ * path matches a registered source's local_path is a per-source cycle in
+ * everything but name, so dream derives the source id up front and passes
+ * it as opts.sourceId — landing the freshness stamp without changing
+ * runCycle's stamp/lock semantics for legacy global callers (the
+ * autopilot-global-maintenance handler runs GLOBAL_PHASES with a brainDir
+ * and MUST NOT stamp per-source freshness; see rejected PR #2549).
  */
-async function resolveSourceForDir(
+export async function resolveSourceForDir(
   engine: BrainEngine,
   brainDir: string | null,
 ): Promise<string | undefined> {

src/core/embed-stale.ts

@@ -20,7 +20,6 @@
 import type { BrainEngine } from './engine.ts';
 import type { ChunkInput } from './types.ts';
 import { embedBatchWithBackoff } from '../commands/embed.ts';
-import { resolveEmbeddingModelLabel } from './embedding.ts';
 import { type DbPacer, createNoopPacer, observed } from './db-pacer.ts';
 import { AbortError } from './abort-check.ts';
 
@@ -201,17 +200,11 @@ export async function embedStaleForSource(
         for (let j = 0; j < stale.length; j++) {
           staleIdxToEmbedding.set(stale[j].chunk_index, embeddings[j]);
         }
-        // #1717: label re-embedded chunks with the model that produced the
-        // vector; preserved chunks keep their existing model. Without this,
-        // upsertChunks falls back to DEFAULT_EMBEDDING_MODEL for every chunk
-        // (the same mislabel the embed.ts paths fixed).
-        const embedModelLabel = resolveEmbeddingModelLabel();
         const merged: ChunkInput[] = existing.map((c) => ({
           chunk_index: c.chunk_index,
           chunk_text: c.chunk_text,
           chunk_source: c.chunk_source,
           embedding: staleIdxToEmbedding.get(c.chunk_index) ?? undefined,
-          model: staleIdxToEmbedding.has(c.chunk_index) && embedModelLabel ? embedModelLabel : c.model,
           token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
           // Carry through per-chunk metadata. upsertChunks writes these as
           // EXCLUDED.<col> (not COALESCE), so omitting them here resets image

src/core/embedding.ts

@@ -113,21 +113,6 @@ export async function embedBatch(
   return results;
 }
 
-/**
- * Resolve the embedding model label (`provider:model`) to stamp onto
- * `content_chunks.model`, so each chunk records the model that actually
- * produced its vector instead of the engine's hardcoded default (#1717).
- * Returns undefined if the gateway is unconfigured; callers then fall back
- * to the chunk's existing model rather than mislabeling it.
- */
-export function resolveEmbeddingModelLabel(): string | undefined {
-  try {
-    return gatewayGetModel();
-  } catch {
-    return undefined;
-  }
-}
-
 /** Currently-configured embedding model (short form without provider prefix). */
 export function getEmbeddingModelName(): string {
   return gatewayGetModel().split(':').slice(1).join(':') || 'text-embedding-3-large';

src/core/import-file.ts

@@ -8,7 +8,7 @@ import { chunkText } from './chunkers/recursive.ts';
 import { chunkCodeText, chunkCodeTextFull, detectCodeLanguage, CHUNKER_VERSION } from './chunkers/code.ts';
 import { findChunkForOffset } from './chunkers/edge-extractor.ts';
 import { extractCodeRefs, imageOfCandidates } from './link-extraction.ts';
-import { embedBatch, embedMultimodal, currentEmbeddingSignature, resolveEmbeddingModelLabel } from './embedding.ts';
+import { embedBatch, embedMultimodal, currentEmbeddingSignature } from './embedding.ts';
 import { slugifyPath, slugifyCodePath, isCodeFilePath } from './sync.ts';
 import type { ChunkInput, PageInput, PageType } from './types.ts';
 import { computeEffectiveDate } from './effective-date.ts';
@@ -716,12 +716,8 @@ export async function importFromContent(
       ? chunks.map((c) => wrapChunkForEmbedding(c.chunk_text, prefix, c.chunk_source))
       : chunks.map((c) => c.chunk_text);
     const embeddings = await embedBatch(wrappedTexts);
-    // #1717: label each chunk with the model that actually produced its
-    // vector, not the engine's hardcoded default.
-    const embedModelLabel = resolveEmbeddingModelLabel();
     for (let i = 0; i < chunks.length; i++) {
       chunks[i].embedding = embeddings[i];
-      if (embedModelLabel) chunks[i].model = embedModelLabel;
       // token_count tracks the wrapped string length so cost reporting
       // reflects what we actually sent to the embedder.
       chunks[i].token_count = Math.ceil(wrappedTexts[i].length / 4);
@@ -1145,10 +1141,7 @@ export async function importCodeFile(
     const matched = existingByKey.get(key);
     if (matched && matched.embedding) {
       // Reuse the existing embedding verbatim. No API call, no cost.
-      // #1717: carry the existing model label along with the reused vector
-      // so the upsert doesn't relabel it with the engine default.
       chunks[i]!.embedding = matched.embedding as Float32Array;
-      chunks[i]!.model = matched.model ?? undefined;
       chunks[i]!.token_count = matched.token_count ?? undefined;
     } else {
       needsEmbedIndexes.push(i);
@@ -1160,12 +1153,9 @@ export async function importCodeFile(
     try {
       const textsToEmbed = needsEmbedIndexes.map((i) => chunks[i]!.chunk_text);
       const embeddings = await embedBatch(textsToEmbed);
-      // #1717: stamp the model that produced these vectors.
-      const embedModelLabel = resolveEmbeddingModelLabel();
       for (let j = 0; j < needsEmbedIndexes.length; j++) {
         const i = needsEmbedIndexes[j]!;
         chunks[i]!.embedding = embeddings[j]!;
-        if (embedModelLabel) chunks[i]!.model = embedModelLabel;
         chunks[i]!.token_count = Math.ceil(chunks[i]!.chunk_text.length / 4);
       }
     } catch (e: unknown) {

test/autopilot-shutdown-engine-close.test.ts

@@ -0,0 +1,63 @@
+/**
+ * #1872 — autopilot SIGTERM/SIGINT must close the engine before exit.
+ *
+ * On PGLite the cycle steps run INLINE in the autopilot process, so a hard
+ * `process.exit` mid-write (systemctl stop → SIGTERM) kills WASM Postgres
+ * with the WAL dirty and can corrupt the brain. Two exit paths must both
+ * close the engine:
+ *
+ *   - autopilot's own shutdown() (owns SIGINT + internal stops like
+ *     max_crashes / cycle-failure-cap), and
+ *   - process-cleanup's SIGTERM handler (installed at cli.ts module load,
+ *     which exits within its 3s cleanup deadline) — reached via the
+ *     registered 'autopilot-engine-close' cleanup callback.
+ *
+ * Because the shutdown path is deep inside `runAutopilot()` (a long-running
+ * daemon loop that ends in process.exit), a behavioral test would have to
+ * spawn + signal a real daemon. Following the established precedent
+ * (test/autopilot-supervisor-wiring.test.ts, test/autopilot-fanout-wiring.test.ts),
+ * these static-shape regressions pin the load-bearing wiring instead.
+ */
+import { describe, expect, it } from 'bun:test';
+import { readFileSync } from 'fs';
+import { join } from 'path';
+
+const AUTOPILOT_SRC = readFileSync(
+  join(import.meta.dir, '..', 'src', 'commands', 'autopilot.ts'),
+  'utf8',
+);
+
+describe('autopilot.ts graceful engine shutdown (#1872)', () => {
+  it('registers an engine-close callback in the process-cleanup registry (SIGTERM path)', () => {
+    // process-cleanup owns SIGTERM (installed at cli.ts:10) and hard-exits
+    // after its cleanup pass; without this registration the engine is never
+    // closed on `systemctl stop`.
+    expect(AUTOPILOT_SRC).toContain(
+      "import { registerCleanup } from '../core/process-cleanup.ts';",
+    );
+    expect(AUTOPILOT_SRC).toContain(
+      "registerCleanup('autopilot-engine-close', closeEngine)",
+    );
+  });
+
+  it('closeEngine aborts the in-flight inline cycle then disconnects the engine', () => {
+    // Abort first (runCycle checks the signal between phases and threads it
+    // into phase sub-work), bounded drain, then disconnect.
+    expect(AUTOPILOT_SRC).toMatch(
+      /const closeEngine = async \(\) => \{[\s\S]{0,900}shutdownAbort\.abort\([\s\S]{0,900}engine\.disconnect\(\)/,
+    );
+  });
+
+  it('the inline runCycle call carries the shutdown abort signal and is tracked as in-flight', () => {
+    // PGLite / --inline path: the cycle runs in-process, so shutdown must be
+    // able to (a) signal it to wind down and (b) await it before closing.
+    expect(AUTOPILOT_SRC).toMatch(/signal:\s*shutdownAbort\.signal/);
+    expect(AUTOPILOT_SRC).toMatch(/inflightInlineCycle\s*=\s*cyclePromise/);
+  });
+
+  it('shutdown() awaits closeEngine() before process.exit(0) (SIGINT + internal-stop path)', () => {
+    expect(AUTOPILOT_SRC).toMatch(
+      /await closeEngine\(\);[\s\S]{0,400}process\.exit\(0\)/,
+    );
+  });
+});

test/dream-dir-source-stamp.test.ts

@@ -0,0 +1,99 @@
+/**
+ * #1869 — `gbrain dream --dir <path>` stamps cycle freshness when the path
+ * matches a registered source's local_path.
+ *
+ * Pre-fix, only `--source <id>` runs wrote last_source_cycle_at /
+ * last_full_cycle_at (runCycle's stamp gate reads opts.sourceId, and dream
+ * never derived one from --dir), so a path-scoped brain showed doctor's
+ * cycle_freshness as perpetually stale.
+ *
+ * The fix lives in dream.ts (derive the source id from the resolved brain
+ * dir via resolveSourceForDir), NOT in runCycle's stamp gate — a runCycle-
+ * wide change would make the autopilot-global-maintenance handler (global
+ * phases, brainDir set, no sourceId) falsely stamp per-source freshness
+ * (the #2194 poisoning class; see rejected PR #2549).
+ *
+ * Same real-PGLite/no-mocks discipline as test/dream.test.ts; same
+ * GBRAIN_HOME isolation as test/cycle-last-full-cycle-at.test.ts (the
+ * cycle's PGLite file lock lives under ~/.gbrain).
+ */
+import { describe, test, expect, beforeAll, afterAll, beforeEach, afterEach } from 'bun:test';
+import { mkdtempSync, rmSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { resetPgliteState } from './helpers/reset-pglite.ts';
+import { runDream } from '../src/commands/dream.ts';
+import { withEnv } from './helpers/with-env.ts';
+
+let engine: PGLiteEngine;
+let brainDir: string;
+let gbrainHome: string;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+}, 60_000);
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+beforeEach(async () => {
+  await resetPgliteState(engine);
+  brainDir = mkdtempSync(join(tmpdir(), 'gbrain-dream-stamp-'));
+  gbrainHome = mkdtempSync(join(tmpdir(), 'gbrain-dream-stamp-home-'));
+}, 60_000);
+
+afterEach(() => {
+  rmSync(brainDir, { recursive: true, force: true });
+  rmSync(gbrainHome, { recursive: true, force: true });
+});
+
+async function seedSource(id: string, archived = false): Promise<void> {
+  await engine.executeRaw(
+    `INSERT INTO sources (id, name, local_path, config, archived, created_at)
+     VALUES ($1, $2, $3, '{}'::jsonb, $4, NOW())`,
+    [id, id, brainDir, archived],
+  );
+}
+
+async function readLastFullCycleAt(sourceId: string): Promise<string | null> {
+  const rows = await engine.executeRaw<{ config: Record<string, unknown> | null }>(
+    `SELECT config FROM sources WHERE id = $1`,
+    [sourceId],
+  );
+  const raw = rows[0]?.config?.last_full_cycle_at;
+  return typeof raw === 'string' ? raw : null;
+}
+
+describe('gbrain dream --dir <path> freshness stamp (#1869)', () => {
+  test('--dir matching a source local_path stamps last_full_cycle_at', async () => {
+    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
+      await seedSource('path-scoped');
+      expect(await readLastFullCycleAt('path-scoped')).toBeNull();
+
+      const report = await runDream(engine, ['--dir', brainDir, '--phase', 'lint', '--json']);
+      expect(report).toBeTruthy();
+      if (report) expect(['ok', 'clean']).toContain(report.status);
+
+      // Pre-fix this stays null forever: dream never passed a sourceId, so
+      // runCycle's stamp gate skipped the write.
+      expect(await readLastFullCycleAt('path-scoped')).not.toBeNull();
+    });
+  }, 60_000);
+
+  test('--dir matching an ARCHIVED source does not stamp it', async () => {
+    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
+      await seedSource('mothballed', true);
+
+      const report = await runDream(engine, ['--dir', brainDir, '--phase', 'lint', '--json']);
+      expect(report).toBeTruthy();
+
+      // Stamping an archived source would mask data staleness when it is
+      // later restored (mirrors the explicit --source archived guard).
+      expect(await readLastFullCycleAt('mothballed')).toBeNull();
+    });
+  }, 60_000);
+});

test/dream.test.ts

@@ -562,12 +562,22 @@ describe('runDream — --source / --source-id (v0.41.13)', () => {
 
   // ─── Back-compat: bare `gbrain dream` does NOT write per-source stamp ─
 
-  test('gbrain dream (no --source) leaves all sources untouched (back-compat regression)', async () => {
-    await seedSource('alpha');
-    await seedSource('beta');
+  test('gbrain dream (no --source) stamps only the source whose local_path matches --dir (#1869)', async () => {
+    // Pre-#1869 this asserted NO source was ever stamped without an explicit
+    // --source — which is exactly the bug: a path-scoped `gbrain dream --dir`
+    // run never landed a freshness stamp and doctor's cycle_freshness stayed
+    // stale forever. New truth: the source whose local_path matches the
+    // resolved brain dir is derived and stamped; unrelated sources stay
+    // untouched (cross-source isolation).
+    await seedSource('alpha'); // local_path = repo → derived + stamped
+    await engine.executeRaw(
+      `INSERT INTO sources (id, name, local_path, config, archived, created_at)
+       VALUES ($1, $2, $3, '{}'::jsonb, false, NOW())`,
+      ['beta', 'beta', '/somewhere/else'],
+    );
     const report = await runDream(engine, ['--dir', repo, '--phase', 'lint', '--json']);
     expect(report).toBeTruthy();
-    expect(await readLastFullCycleAt('alpha')).toBeNull();
+    expect(await readLastFullCycleAt('alpha')).not.toBeNull();
     expect(await readLastFullCycleAt('beta')).toBeNull();
   }, 60_000);
 

test/embed-stale.serial.test.ts

@@ -15,7 +15,6 @@ import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:tes
 import { PGLiteEngine } from '../src/core/pglite-engine.ts';
 import { resetPgliteState } from './helpers/reset-pglite.ts';
 import { embedStaleForSource } from '../src/core/embed-stale.ts';
-import { configureGateway, resetGateway } from '../src/core/ai/gateway.ts';
 import type { ChunkInput } from '../src/core/types.ts';
 
 let engine: PGLiteEngine;
@@ -277,49 +276,4 @@ describe('embedStaleForSource', () => {
     // The stale text row actually got its embedding.
     expect(txtRow.embedded_at).not.toBeNull();
   });
-
-  // #1717: the backfill path must label re-embedded chunks with the model
-  // that produced the vector, and preserve the existing label on chunks it
-  // did not touch (before the fix, both were reset to the engine default).
-  test('labels re-embedded chunks with the gateway model, preserves untouched labels (#1717)', async () => {
-    configureGateway({
-      embedding_model: 'openai:text-embedding-3-large',
-      env: { OPENAI_API_KEY: 'sk-test-embed-stale-1717' },
-    });
-    try {
-      await engine.putPage('notes/model-label', {
-        type: 'note',
-        title: 'model-label',
-        compiled_truth: '# model-label\n\nseeded',
-      });
-      await engine.upsertChunks('notes/model-label', [
-        {
-          chunk_index: 0,
-          chunk_text: 'already embedded elsewhere',
-          chunk_source: 'compiled_truth',
-          embedding: new Float32Array(1536).fill(0.01),
-          model: 'voyage:voyage-3',
-          token_count: 4,
-        },
-        {
-          chunk_index: 1,
-          chunk_text: 'stale chunk needing embed',
-          chunk_source: 'compiled_truth',
-          token_count: 5,
-          embedding: undefined, // stale
-        },
-      ]);
-
-      const result = await embedStaleForSource(engine, 'default', { embedFn: fakeEmbedFn });
-      expect(result.embedded).toBe(1);
-
-      const after = await engine.getChunks('notes/model-label');
-      const preserved = after.find((c) => c.chunk_index === 0)!;
-      const reembedded = after.find((c) => c.chunk_index === 1)!;
-      expect(reembedded.model).toBe('openai:text-embedding-3-large');
-      expect(preserved.model).toBe('voyage:voyage-3');
-    } finally {
-      resetGateway();
-    }
-  });
 });

test/embed.serial.test.ts

@@ -37,8 +37,6 @@ mock.module('../src/core/embedding.ts', () => ({
   // setPageEmbeddingSignature / invalidateStaleSignatureEmbeddings resolve to
   // null via the Proxy default, so the signature value is inert here.
   currentEmbeddingSignature: () => 'test:model:1536',
-  // #1717: embed paths stamp this label on (re)embedded chunks.
-  resolveEmbeddingModelLabel: () => 'openai:text-embedding-3-large',
 }));
 
 // Import AFTER mocking.
@@ -805,34 +803,3 @@ describe('embedAllStale --source threading (D7)', () => {
     expect((firstCallOpts as { sourceId?: string }).sourceId).toBe('media-corpus');
   });
 });
-
-// #1717: content_chunks.model must record the model that actually produced
-// each vector, not the gateway/engine default.
-describe('content_chunks.model labeling (#1717)', () => {
-  test('stamps the resolved embedding model on re-embedded chunks, preserves it on untouched chunks', async () => {
-    let upserted: any[] | undefined;
-    // Chunk 0 is stale (no embedded_at) → gets re-embedded this pass.
-    // Chunk 1 is already embedded with a DIFFERENT model → must be preserved,
-    // not relabeled to the current model.
-    const chunks = [
-      { chunk_index: 0, chunk_text: 'a', chunk_source: 'compiled_truth', embedded_at: null, model: 'zeroentropyai:zembed-1', token_count: 1 },
-      { chunk_index: 1, chunk_text: 'b', chunk_source: 'compiled_truth', embedded_at: '2026-01-01', embedding: new Float32Array(1536), model: 'voyage:voyage-3', token_count: 1 },
-    ];
-    const engine = mockEngine({
-      getPage: async () => ({ slug: 'notes/x', compiled_truth: 'a', timeline: '', source_id: 'default' }),
-      getChunks: async () => chunks,
-      upsertChunks: async (_slug: string, c: any[]) => { upserted = c; },
-      setPageEmbeddingSignature: async () => null,
-    });
-
-    await runEmbedCore(engine, { slugs: ['notes/x'] });
-
-    expect(upserted).toBeDefined();
-    const byIdx = Object.fromEntries(upserted!.map(c => [c.chunk_index, c]));
-    // Re-embedded chunk carries the model that produced its vector (was
-    // mislabeled with the default before the fix).
-    expect(byIdx[0].model).toBe('openai:text-embedding-3-large');
-    // Untouched chunk keeps its original model — no wholesale relabel.
-    expect(byIdx[1].model).toBe('voyage:voyage-3');
-  });
-});

test/import-signature-stamp.serial.test.ts

@@ -73,21 +73,4 @@ describe('importFromContent embedding_signature stamping (F1)', () => {
     await importFromContent(engine, 'concepts/unstamped', '# Unstamped\n\nbody content.', { noEmbed: true });
     expect(await signatureOf('concepts/unstamped')).toBeNull();
   });
-
-  // #1717: content_chunks.model must record the model that produced the
-  // vector (the configured gateway model), not the engine's hardcoded
-  // default. The gateway here is configured to openai:text-embedding-3-large,
-  // which differs from DEFAULT_EMBEDDING_MODEL — so this fails without the
-  // import-path model stamping.
-  test('inline embed labels content_chunks.model with the configured model (#1717)', async () => {
-    await importFromContent(engine, 'concepts/labeled', '# Labeled\n\nsome body content to chunk and embed.', {});
-    const rows = await engine.executeRaw<{ model: string }>(
-      `SELECT cc.model FROM content_chunks cc
-        JOIN pages p ON p.id = cc.page_id
-       WHERE p.slug = $1 AND p.source_id = 'default'`,
-      ['concepts/labeled'],
-    );
-    expect(rows.length).toBeGreaterThan(0);
-    for (const r of rows) expect(r.model).toBe('openai:text-embedding-3-large');
-  });
 });