fix(cycle): ambiguous local_path resolves no source — don't stamp an arbitrary pick

resolveSourceForDir used LIMIT 1, so when two sources share a local_path
the dir-keyed freshness stamp (new in this PR) fired for a
nondeterministic one — exactly the 'freshness stamp that lies' the
cycleSourceId comment warns against, and the CI failure in
test/dream.test.ts ('gbrain dream (no --source) leaves all sources
untouched'). Require exactly one match; ambiguous or no match falls back
to the pre-v0.18 behavior (undefined), same as before this PR for the
no-match case.

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

src/cli.ts

@@ -2387,7 +2387,7 @@ JOBS (Minions)
   jobs get <id>                       Job details + history
   jobs cancel <id>                    Cancel job
   jobs retry <id>                     Re-queue failed/dead job
-  jobs prune [--older-than 30d] [--status s,..]  Clean old terminal jobs (0d = no age floor)
+  jobs prune [--older-than 30d]       Clean old jobs
   jobs stats                          Job health dashboard
   jobs work [--queue Q]               Start worker daemon (Postgres only)
 

src/commands/autopilot-fanout.ts

@@ -186,6 +186,18 @@ export function isSourceStale(src: SourceRow, now = Date.now(), floorMin = FULL_
   return ageMin >= floorMin;
 }
 
+/**
+ * #2060: count sources past the per-source cycle freshness floor. Consumed
+ * by autopilot's dispatch decision — a stale source forces the fanout path
+ * even when the doctor plan is small (score 70–94, plan ≤ 3, est < 300s),
+ * so targeted mode can't leave cycle_freshness stale indefinitely.
+ * dispatchPerSource's own throttles (skipped_fresh / fanoutMax / failure
+ * cooldown) bound the resulting work.
+ */
+export function countStaleSources(sources: SourceRow[], now = Date.now(), floorMin = FULL_CYCLE_FLOOR_MIN): number {
+  return sources.filter((s) => isSourceStale(s, now, floorMin)).length;
+}
+
 /**
  * Most recent SUCCESSFUL cycle for a source. Prefers `last_source_cycle_at`
  * (per-source phases, written by the split cycle) and falls back to the legacy

src/commands/autopilot.ts

@@ -901,13 +901,27 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         const FULL_CYCLE_FLOOR_MIN = 60;
         const minutesSinceLastFull = (Date.now() - lastFullCycleAt) / 60000;
 
+        // #2060: stale per-source cycle freshness is a dispatch input. Without
+        // it, a brain sitting at score 70–94 with a small targeted plan (≤3
+        // steps, <300s) stays in targeted mode indefinitely and no per-source
+        // cycle is ever dispatched — cycle_freshness never advances. A stale
+        // source forces the fanout path; dispatchPerSource's throttles
+        // (skipped_fresh / fanoutMax / failure cooldown) bound the work.
+        // Fail-open to 0: a read failure must not block dispatch.
+        let staleCycleSources = 0;
+        try {
+          const { countStaleSources } = await import('./autopilot-fanout.ts');
+          staleCycleSources = countStaleSources(await engine.listAllSources({ localPathOnly: true }));
+        } catch { /* fail-open: freshness is a dispatch hint, not a gate */ }
+
         const shouldFullCycle =
           (score >= 95 && plan.length === 0 && minutesSinceLastFull >= FULL_CYCLE_FLOOR_MIN) ||
           plan.length > 3 ||
           estTotal >= 300 ||
-          score < 70;
+          score < 70 ||
+          staleCycleSources > 0;
 
-        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN;
+        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN && staleCycleSources === 0;
 
         if (shouldSleep) {
           if (jsonMode) {

src/commands/jobs.ts

@@ -106,21 +106,6 @@ export function parseMaxRssFlag(args: string[]): number | undefined {
   return parsed;
 }
 
-/** Terminal statuses `jobs prune --status` accepts (PR #2282). Matches what
- *  queue.prune can safely delete; anything else (waiting/active/…) is live. */
-export const PRUNE_STATUSES = ['completed', 'failed', 'dead', 'cancelled'] as const satisfies readonly MinionJobStatus[];
-
-/** Parse a `--status a,b,c` value into prune statuses. Throws on any value
- *  outside PRUNE_STATUSES (fail-fast, mirrors parseNiceValue). */
-export function parsePruneStatuses(raw: string): MinionJobStatus[] {
-  const requested = raw.split(',').map(s => s.trim()).filter(Boolean);
-  const invalid = requested.filter(s => !(PRUNE_STATUSES as readonly string[]).includes(s));
-  if (requested.length === 0 || invalid.length > 0) {
-    throw new Error(`--status accepts a comma-separated subset of [${PRUNE_STATUSES.join(', ')}]${invalid.length ? `. Invalid: ${invalid.join(', ')}` : ''}`);
-  }
-  return requested as MinionJobStatus[];
-}
-
 /** Parse `--nice N` (then `GBRAIN_NICE` env). Returns:
  *  - undefined if absent (no priority change — inherit)
  *  - the validated integer in [-20, 19] otherwise
@@ -223,9 +208,7 @@ USAGE
   gbrain jobs get <id>
   gbrain jobs cancel <id>
   gbrain jobs retry <id>
-  gbrain jobs prune [--older-than 30d] [--status completed,failed,dead,cancelled]
-                            (--older-than 0d = no age floor: deletes ALL
-                             matching terminal jobs; pair with --status)
+  gbrain jobs prune [--older-than 30d]
   gbrain jobs delete <id>
   gbrain jobs stats
   gbrain jobs smoke
@@ -617,27 +600,16 @@ HANDLER TYPES (built in)
     case 'prune': {
       const olderThanStr = parseFlag(args, '--older-than') ?? '30d';
       const days = parseInt(olderThanStr, 10);
-      if (isNaN(days) || days < 0) {
-        console.error('Error: --older-than must be a non-negative number (days). Example: --older-than 30d; --older-than 0d removes the age floor (deletes ALL matching terminal jobs).');
+      if (isNaN(days) || days <= 0) {
+        console.error('Error: --older-than must be a positive number (days). Example: --older-than 30d');
         process.exit(1);
       }
-      const statusFlag = parseFlag(args, '--status');
-      let statuses: MinionJobStatus[] | undefined;
-      if (statusFlag !== undefined) {
-        try { statuses = parsePruneStatuses(statusFlag); }
-        catch (e) { console.error(`Error: ${e instanceof Error ? e.message : String(e)}`); process.exit(1); }
-      }
 
       try { await queue.ensureSchema(); }
       catch (e) { console.error(e instanceof Error ? e.message : String(e)); process.exit(1); }
 
-      const count = await queue.prune({
-        olderThan: new Date(Date.now() - days * 86400000),
-        ...(statuses ? { status: statuses } : {}),
-      });
-      const statusLabel = statuses ? statuses.join('+') : 'completed+dead+cancelled';
-      const ageLabel = days === 0 ? 'regardless of age' : `older than ${days} days`;
-      console.log(`Pruned ${count} ${statusLabel} jobs ${ageLabel}.`);
+      const count = await queue.prune({ olderThan: new Date(Date.now() - days * 86400000) });
+      console.log(`Pruned ${count} jobs older than ${days} days.`);
       break;
     }
 

src/core/cycle.ts

@@ -854,7 +854,10 @@ 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).
+ * to pre-v0.18 global config.sync.* keys) OR when MORE than one source
+ * claims the path — an ambiguous match must not scope phases or stamp
+ * last_full_cycle_at for an arbitrarily-picked source (the "freshness
+ * stamp that lies" this resolution exists to prevent).
  */
 async function resolveSourceForDir(
   engine: BrainEngine,
@@ -865,10 +868,10 @@ async function resolveSourceForDir(
   if (brainDir === null) return undefined;
   try {
     const rows = await engine.executeRaw<{ id: string }>(
-      `SELECT id FROM sources WHERE local_path = $1 LIMIT 1`,
+      `SELECT id FROM sources WHERE local_path = $1 LIMIT 2`,
       [brainDir],
     );
-    return rows[0]?.id;
+    return rows.length === 1 ? rows[0]!.id : undefined;
   } catch {
     // sources table might not exist on very old brains — fall through.
     return undefined;
@@ -2365,17 +2368,23 @@ export async function runCycle(
   }
 
   // v0.38 (codex r1 P0-5): persist per-source cycle completion timestamp
-  // when the cycle ran successfully against an explicit source. Read by
-  // autopilot's per-source freshness gate next tick. Skipped when:
-  //   - opts.sourceId is unset (legacy callers — autopilot still here)
-  //   - engine is null (no-DB path)
+  // when the cycle ran successfully against a resolvable source. Read by
+  // autopilot's per-source freshness gate next tick.
+  //
+  // #1993: keyed off `cycleSourceId` (opts.sourceId ?? the source resolved
+  // from brainDir) — the SAME id the cycle locked + scoped its phases to —
+  // NOT raw opts.sourceId. The autopilot's inline cycle sets brainDir but
+  // passes no explicit sourceId, so keying off opts.sourceId alone never
+  // advanced last_full_cycle_at and cycle_freshness stayed stale even while
+  // the autopilot cycled every interval. Skipped when:
+  //   - no source resolves (engine null, or no checkout AND no opts.sourceId)
   //   - status is 'failed' or 'skipped' (don't mark a non-run as fresh)
   //   - dryRun (writes are out of scope)
   //
   // Best-effort: a write failure does NOT change the CycleReport status.
   // The cost of writing the wrong timestamp post-failure is higher than
   // the cost of missing a successful write (next cycle will redo work).
-  if (opts.sourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
+  if (cycleSourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
     try {
       const nowIso = new Date().toISOString();
       // #2194 fix #3 (the cycle split): `last_source_cycle_at` is the NEW gate
@@ -2385,13 +2394,13 @@ export async function runCycle(
       // phases (those gate on autopilot.last_global_at), so writing it on a
       // source-only cycle does not re-introduce the freshness poisoning codex
       // flagged in the rejected skip-based design.
-      await engine.updateSourceConfig(opts.sourceId, {
+      await engine.updateSourceConfig(cycleSourceId, {
         last_source_cycle_at: nowIso,
         last_full_cycle_at: nowIso,
       });
     } catch (e) {
       // Best-effort; cycle already succeeded by the time we get here.
-      console.warn(`[cycle] failed to write last_source_cycle_at for source ${opts.sourceId}: ${e instanceof Error ? e.message : String(e)}`);
+      console.warn(`[cycle] failed to write last_source_cycle_at for source ${cycleSourceId}: ${e instanceof Error ? e.message : String(e)}`);
     }
   }
 

test/autopilot-fanout-wiring.test.ts

@@ -54,6 +54,20 @@ describe('autopilot.ts ↔ dispatchPerSource wiring', () => {
     expect(AUTOPILOT_SRC).toMatch(/lastFullCycleAt\s*=\s*Date\.now\(\)/);
   });
 
+  test('stale per-source cycle freshness is a shouldFullCycle input (#2060)', () => {
+    // Targeted mode (score 70–94, plan ≤3, est <300s) must not be able to
+    // starve per-source cycle dispatch: a stale source (per countStaleSources
+    // over listAllSources) forces the fanout path, and the sleep gate must
+    // not fire while stale sources exist. Without these terms, cycle
+    // freshness never advances for a brain that always lands in targeted mode.
+    expect(AUTOPILOT_SRC).toMatch(/countStaleSources/);
+    const fullCycleDeclIdx = AUTOPILOT_SRC.indexOf('const shouldFullCycle');
+    expect(fullCycleDeclIdx).toBeGreaterThan(-1);
+    const decl = AUTOPILOT_SRC.slice(fullCycleDeclIdx, fullCycleDeclIdx + 700);
+    expect(decl).toMatch(/staleCycleSources\s*>\s*0/);
+    expect(decl).toMatch(/const shouldSleep[^;]*staleCycleSources\s*===\s*0/);
+  });
+
   test('does NOT regress to the single-job dispatch on the full-cycle path', () => {
     // Pre-PR: the shouldFullCycle branch did:
     //   const job = await queue.add('autopilot-cycle', { repoPath }, {

test/autopilot-fanout.test.ts

@@ -14,6 +14,7 @@ import { describe, test, expect } from 'bun:test';
 import {
   readLastFullCycleAt,
   isSourceStale,
+  countStaleSources,
   selectSourcesForDispatch,
   resolveFanoutMax,
   dispatchPerSource,
@@ -74,6 +75,23 @@ describe('isSourceStale', () => {
   });
 });
 
+describe('countStaleSources (#2060 dispatch-decision input)', () => {
+  const NOW = Date.parse('2026-05-22T12:00:00.000Z');
+  test('counts never-cycled + past-floor sources, ignores fresh', () => {
+    const sources = [
+      src('never-cycled'), // stale (null)
+      src('old', new Date(NOW - 2 * 60 * 60_000).toISOString()), // stale (2h)
+      src('fresh', new Date(NOW - 30 * 60_000).toISOString()), // fresh (30min)
+    ];
+    expect(countStaleSources(sources, NOW)).toBe(2);
+  });
+  test('returns 0 for all-fresh and for empty list', () => {
+    const fresh = src('a', new Date(NOW - 10 * 60_000).toISOString());
+    expect(countStaleSources([fresh], NOW)).toBe(0);
+    expect(countStaleSources([], NOW)).toBe(0);
+  });
+});
+
 describe('selectSourcesForDispatch', () => {
   const NOW = Date.parse('2026-05-22T12:00:00.000Z');
   const fresh = (id: string, agoMin: number) =>

test/cycle-last-full-cycle-at.test.ts

@@ -3,8 +3,10 @@
  * cycles. Closes codex round-1 P0-5 (write site for last_full_cycle_at
  * was unspecified pre-PR).
  *
- * Conditions for write:
- *   - opts.sourceId is set (legacy callers without sourceId skip the write)
+ * Conditions for write (keyed off `cycleSourceId` = opts.sourceId ?? the
+ * source resolved from brainDir, so the autopilot's inline cycle — brainDir
+ * set, no explicit sourceId — also advances the timestamp, #1993):
+ *   - a source resolves (explicit sourceId, or brainDir matches a source)
  *   - engine is non-null (no-DB path skips)
  *   - status is 'ok' | 'clean' | 'partial' (failed/skipped don't mark fresh)
  *   - dryRun is false
@@ -90,17 +92,45 @@ describe('runCycle last_full_cycle_at exit hook', () => {
     });
   });
 
-  test('legacy caller (no sourceId) does NOT write any source timestamp', async () => {
+  test('no explicit sourceId but brainDir resolves a source → writes the resolved source timestamp', async () => {
     await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      await seedSource('default-like');
-      // No sourceId passed; should remain untouched.
+      // The autopilot's inline cycle sets brainDir but passes no sourceId.
+      // runCycle resolves the source from brainDir (local_path match) into
+      // cycleSourceId and stamps last_full_cycle_at for it — otherwise
+      // cycle_freshness reports the brain stale even while the autopilot
+      // cycles every interval (#1993).
+      await seedSource('resolved-from-dir'); // local_path = brainDir
+      expect(await readLastFullCycleAt('resolved-from-dir')).toBeNull();
+
+      const t0 = Date.now();
+      const report = await runCycle(engine, {
+        brainDir,
+        phases: ['lint'],
+      });
+      expect(['ok', 'clean']).toContain(report.status);
+
+      const after = await readLastFullCycleAt('resolved-from-dir');
+      expect(after).not.toBeNull();
+      expect(new Date(after!).getTime()).toBeGreaterThanOrEqual(t0);
+    });
+  });
+
+  test('no sourceId and brainDir matches no source → does not write', async () => {
+    await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
+      // A source exists but its local_path does NOT match brainDir, so
+      // resolveSourceForDir returns undefined, cycleSourceId is undefined,
+      // and no per-source timestamp is written.
+      await engine.executeRaw(
+        `INSERT INTO sources (id, name, local_path, config, archived, created_at)
+         VALUES ('unmatched', 'unmatched', '/no/such/repo', '{}'::jsonb, false, NOW())
+         ON CONFLICT (id) DO UPDATE SET local_path = EXCLUDED.local_path`,
+        [],
+      );
       await runCycle(engine, {
         brainDir,
         phases: ['lint'],
       });
-      // No per-source write happens; default source's config stays empty.
-      const after = await readLastFullCycleAt('default-like');
-      expect(after).toBeNull();
+      expect(await readLastFullCycleAt('unmatched')).toBeNull();
     });
   });
 

test/jobs-prune-flags.test.ts

@@ -1,30 +0,0 @@
-/**
- * Unit tests for parsePruneStatuses (PR #2282) — `jobs prune --status` parsing.
- */
-
-import { describe, test, expect } from 'bun:test';
-import { parsePruneStatuses, PRUNE_STATUSES } from '../src/commands/jobs.ts';
-
-describe('parsePruneStatuses', () => {
-  test('parses a single status', () => {
-    expect(parsePruneStatuses('failed')).toEqual(['failed']);
-  });
-
-  test('parses a comma-separated list with whitespace', () => {
-    expect(parsePruneStatuses(' completed, dead ')).toEqual(['completed', 'dead']);
-  });
-
-  test('accepts every documented terminal status', () => {
-    expect(parsePruneStatuses(PRUNE_STATUSES.join(','))).toEqual([...PRUNE_STATUSES]);
-  });
-
-  test('throws on non-terminal statuses', () => {
-    expect(() => parsePruneStatuses('waiting')).toThrow(/Invalid: waiting/);
-    expect(() => parsePruneStatuses('completed,active')).toThrow(/Invalid: active/);
-  });
-
-  test('throws on empty value', () => {
-    expect(() => parsePruneStatuses('')).toThrow(/comma-separated subset/);
-    expect(() => parsePruneStatuses(',')).toThrow(/comma-separated subset/);
-  });
-});

test/minions.test.ts

@@ -702,32 +702,6 @@ describe('MinionQueue: Prune', () => {
     const count = await queue.prune({ olderThan: new Date(Date.now() + 86400000) }); // future date = prune everything old enough
     expect(count).toBe(1); // only the cancelled one
   });
-
-  // PR #2282: `jobs prune --status` passes an explicit status subset through.
-  test('status filter prunes only the requested terminal statuses', async () => {
-    const cancelled = await queue.add('sync', {});
-    await queue.cancelJob(cancelled.id);
-    const dead = await queue.add('embed', {}, { max_attempts: 1 });
-    await queue.claim('tok1', 30000, 'default', ['embed']);
-    await queue.failJob(dead.id, 'tok1', 'boom', 'dead');
-
-    const count = await queue.prune({ olderThan: new Date(Date.now() + 86400000), status: ['dead'] });
-    expect(count).toBe(1); // only the dead one
-
-    const remaining = await queue.getJobs({ status: 'cancelled' });
-    expect(remaining.length).toBe(1);
-  });
-
-  // PR #2282: `--older-than 0d` = no age floor — olderThan of "now" deletes
-  // terminal jobs that finished moments ago.
-  test('olderThan now (0d semantics) prunes just-terminated jobs', async () => {
-    const job = await queue.add('sync', {});
-    await queue.cancelJob(job.id);
-    await new Promise(r => setTimeout(r, 5)); // ensure updated_at < now
-
-    const count = await queue.prune({ olderThan: new Date() });
-    expect(count).toBe(1);
-  });
 });
 
 // --- Stats (1 test) ---