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.
@@ -151,100 +152,6 @@ export function shouldSpawnAutopilotWorker(args: string[]): boolean {
   return !args.includes('--no-worker');
 }
 
-/**
- * #1525 — positional subcommand translation.
- *
- * Pre-fix, `gbrain autopilot status` silently fell through to "start daemon"
- * because `runAutopilot()` only branched on flag forms (`--status`, etc.).
- * `status` was treated as a stray positional and ignored.
- *
- * This translator maps known positional subcommands to their flag form so
- * `autopilot status` is equivalent to `autopilot --status`, then rejects
- * any unrecognized positional with a fail-loud error before any side
- * effect (lockfile, daemon spawn, sync dispatch) runs.
- *
- * Scope decisions:
- *   - Known aliases: `status` → `--status`, `install` → `--install`,
- *     `uninstall` → `--uninstall`, `start` → (drop; default daemon launch).
- *   - `stop` is intentionally NOT aliased here. Stopping a running daemon
- *     is a new behavior (read PID from lock, SIGTERM, drain) that deserves
- *     its own design and PR. Users typing `gbrain autopilot stop` today get
- *     the unknown-positional error with the canonical alternatives.
- *   - At most one positional allowed; multiple positionals fail loud.
- */
-// Every flag that consumes the NEXT argv token. Missing one here makes the
-// translator misread the flag's value as a positional subcommand and exit 2
-// (e.g. `--install --target linux-cron`). Keep in sync with parseArg call sites.
-const AUTOPILOT_VALUE_FLAGS = new Set(['--repo', '--interval', '--target']);
-const AUTOPILOT_POSITIONAL_ALIASES: Record<string, string | null> = {
-  status: '--status',
-  install: '--install',
-  uninstall: '--uninstall',
-  start: null, // drop the positional; default behavior is daemon launch
-};
-
-export type PositionalTranslation =
-  | { ok: true; args: string[] }
-  | {
-      ok: false;
-      reason: 'unknown_subcommand' | 'multiple_subcommands';
-      message: string;
-    };
-
-export function translatePositionalSubcommands(args: string[]): PositionalTranslation {
-  const out: string[] = [];
-  let positionalSeen = false;
-  let i = 0;
-  while (i < args.length) {
-    const a = args[i];
-    if (AUTOPILOT_VALUE_FLAGS.has(a)) {
-      // Pass through the flag and its value untouched. If the value is
-      // missing at end-of-argv, fall through so the existing parseArg
-      // path can report the broken usage.
-      out.push(a);
-      if (i + 1 < args.length) {
-        out.push(args[i + 1]);
-        i += 2;
-      } else {
-        i += 1;
-      }
-      continue;
-    }
-    if (a.startsWith('-')) {
-      out.push(a);
-      i += 1;
-      continue;
-    }
-    // Positional subcommand.
-    if (positionalSeen) {
-      const known = Object.keys(AUTOPILOT_POSITIONAL_ALIASES).join(', ');
-      return {
-        ok: false,
-        reason: 'multiple_subcommands',
-        message: `Multiple subcommands given. Use only one of: ${known}.`,
-      };
-    }
-    positionalSeen = true;
-    if (a in AUTOPILOT_POSITIONAL_ALIASES) {
-      const alias = AUTOPILOT_POSITIONAL_ALIASES[a];
-      if (alias) out.push(alias);
-      i += 1;
-      continue;
-    }
-    const known = Object.keys(AUTOPILOT_POSITIONAL_ALIASES).join(', ');
-    return {
-      ok: false,
-      reason: 'unknown_subcommand',
-      message:
-        `Unknown subcommand: \`${a}\`.\n` +
-        `Allowed subcommands: ${known}.\n` +
-        `Or use the flag form: --status, --install, --uninstall.\n` +
-        `Run \`gbrain autopilot --help\` for full usage.`,
-    };
-  }
-  return { ok: true, args: out };
-}
-
 export function isPidAlive(pid: number): boolean {
   if (!Number.isFinite(pid) || pid <= 0) return false;
   try {
@@ -457,11 +364,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       '       gbrain autopilot --install [--repo <path>]\n' +
       '       gbrain autopilot --uninstall\n' +
       '       gbrain autopilot --status [--json]\n\n' +
-      'Subcommand aliases:\n' +
-      '       gbrain autopilot status     → --status\n' +
-      '       gbrain autopilot install    → --install\n' +
-      '       gbrain autopilot uninstall  → --uninstall\n' +
-      '       gbrain autopilot start      → (default daemon launch)\n\n' +
       'Self-maintaining brain daemon. Runs the full maintenance cycle\n' +
       '(lint + backlinks + sync + extract + embed + orphans) on an interval.\n\n' +
       'For a one-shot cron-triggered cycle, see `gbrain dream`.',
@@ -469,16 +371,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
     return;
   }
 
-  // #1525: translate positional subcommands to their flag form BEFORE any
-  // side effect (lockfile, daemon spawn, sync dispatch). Unknown positionals
-  // fail loud here rather than silently starting the daemon.
-  const translated = translatePositionalSubcommands(args);
-  if (!translated.ok) {
-    console.error(translated.message);
-    process.exit(2);
-  }
-  args = translated.args;
-
   if (args.includes('--install')) {
     await installDaemon(engine, args);
     return;
@@ -542,6 +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
@@ -629,6 +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);
   };
@@ -1117,16 +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/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> {

test/autopilot-positional-subcommands.test.ts

@@ -1,197 +0,0 @@
-/**
- * Tests for translatePositionalSubcommands() — the v0.41.x #1525 fix that
- * prevents `gbrain autopilot status` from silently starting the daemon.
- *
- * IRON RULE regression guard: the exact ticket repro (`gbrain autopilot
- * status`) MUST translate to `--status`, not fall through to the default
- * daemon launch. Verified by the "ticket-exact repro" case below.
- */
-
-import { describe, test, expect } from 'bun:test';
-import { translatePositionalSubcommands } from '../src/commands/autopilot.ts';
-
-describe('translatePositionalSubcommands — known aliases', () => {
-  test('IRON RULE — `autopilot status` translates to `--status` (ticket #1525 repro)', () => {
-    const r = translatePositionalSubcommands(['status']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--status']);
-  });
-
-  test('`install` translates to `--install`', () => {
-    const r = translatePositionalSubcommands(['install']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--install']);
-  });
-
-  test('`uninstall` translates to `--uninstall`', () => {
-    const r = translatePositionalSubcommands(['uninstall']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--uninstall']);
-  });
-
-  test('`start` drops the positional (default daemon launch)', () => {
-    const r = translatePositionalSubcommands(['start']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual([]);
-  });
-
-  test('`start --json` drops only the positional, keeps the flag', () => {
-    const r = translatePositionalSubcommands(['start', '--json']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--json']);
-  });
-});
-
-describe('translatePositionalSubcommands — flag/positional interleaving', () => {
-  test('`status --json` preserves the trailing flag', () => {
-    const r = translatePositionalSubcommands(['status', '--json']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--status', '--json']);
-  });
-
-  test('`--json status` preserves the leading flag', () => {
-    const r = translatePositionalSubcommands(['--json', 'status']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--json', '--status']);
-  });
-
-  test('`--repo /foo status` does not mis-classify the path as positional', () => {
-    const r = translatePositionalSubcommands(['--repo', '/foo', 'status']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--repo', '/foo', '--status']);
-  });
-
-  test('`--interval 300 install` does not mis-classify the number as positional', () => {
-    const r = translatePositionalSubcommands(['--interval', '300', 'install']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--interval', '300', '--install']);
-  });
-
-  test('`--install --target linux-cron` does not mis-classify the target as positional', () => {
-    // --target is installDaemon's value flag; its value must never be read
-    // as a positional subcommand (regression guard for the review fix).
-    const r = translatePositionalSubcommands(['--install', '--target', 'linux-cron']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--install', '--target', 'linux-cron']);
-  });
-
-  test('`install --target macos` keeps the alias translation and the target value', () => {
-    const r = translatePositionalSubcommands(['install', '--target', 'macos']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--install', '--target', 'macos']);
-  });
-
-  test('value-flag at end of argv with missing value passes through (so parseArg can report it)', () => {
-    const r = translatePositionalSubcommands(['--repo']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--repo']);
-  });
-
-  test('value-flag whose value looks like an alias is NOT translated', () => {
-    // `--repo status` means "use repo path 'status'", not "show status".
-    // Translator must not destructure the value of --repo.
-    const r = translatePositionalSubcommands(['--repo', 'status']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--repo', 'status']);
-  });
-});
-
-describe('translatePositionalSubcommands — pass-through cases', () => {
-  test('empty args returns empty args', () => {
-    const r = translatePositionalSubcommands([]);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual([]);
-  });
-
-  test('flag-only invocation passes through unchanged', () => {
-    const r = translatePositionalSubcommands(['--status', '--json']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['--status', '--json']);
-  });
-
-  test('short flag `-h` passes through unchanged', () => {
-    const r = translatePositionalSubcommands(['-h']);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(['-h']);
-  });
-
-  test('all known bare flags pass through unchanged', () => {
-    const flags = ['--help', '--install', '--uninstall', '--status', '--json', '--inline', '--no-worker'];
-    const r = translatePositionalSubcommands(flags);
-    expect(r.ok).toBe(true);
-    if (r.ok) expect(r.args).toEqual(flags);
-  });
-});
-
-describe('translatePositionalSubcommands — rejection of unknown positionals', () => {
-  test('unknown positional `foo` fails with reason=unknown_subcommand + structured message', () => {
-    const r = translatePositionalSubcommands(['foo']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('unknown_subcommand');
-      expect(r.message).toContain('Unknown subcommand: `foo`');
-      expect(r.message).toContain('status');
-      expect(r.message).toContain('install');
-      expect(r.message).toContain('uninstall');
-      expect(r.message).toContain('--help');
-    }
-  });
-
-  test('unknown positional `stop` fails with reason=unknown_subcommand (NOT silently aliased)', () => {
-    // Stop is mentioned in the ticket but deliberately NOT aliased in this
-    // PR — stopping a running daemon is a new behavior, not just an alias.
-    // Until that feature lands separately, `stop` must fail loud rather
-    // than starting the daemon (the bug we're fixing).
-    const r = translatePositionalSubcommands(['stop']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('unknown_subcommand');
-      expect(r.message).toContain('Unknown subcommand: `stop`');
-    }
-  });
-
-  test('unknown positional `status-detail` (close-but-not-matching) fails', () => {
-    const r = translatePositionalSubcommands(['status-detail']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('unknown_subcommand');
-      expect(r.message).toContain('Unknown subcommand: `status-detail`');
-    }
-  });
-
-  test('multiple positionals fail with reason=multiple_subcommands (`start install`)', () => {
-    const r = translatePositionalSubcommands(['start', 'install']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('multiple_subcommands');
-      expect(r.message).toContain('Multiple subcommands');
-    }
-  });
-
-  test('multiple positionals fail even when both are known aliases (`status install`)', () => {
-    const r = translatePositionalSubcommands(['status', 'install']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('multiple_subcommands');
-      expect(r.message).toContain('Multiple subcommands');
-    }
-  });
-
-  test('known-then-unknown rejects with multiple_subcommands (first-positional-wins)', () => {
-    // First positional is known, second is not. Rejection comes from the
-    // multiple-positional rule, which fires before the unknown check; the
-    // intent is "only one subcommand allowed."
-    const r = translatePositionalSubcommands(['status', 'garbage']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) expect(r.reason).toBe('multiple_subcommands');
-  });
-
-  test('unknown-then-known rejects on the unknown (unknown fires before second-positional check)', () => {
-    const r = translatePositionalSubcommands(['garbage', 'status']);
-    expect(r.ok).toBe(false);
-    if (!r.ok) {
-      expect(r.reason).toBe('unknown_subcommand');
-      expect(r.message).toContain('garbage');
-    }
-  });
-});

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);