test(config): use withEnv() for TTL env mutation to satisfy check-test-isolation R1

CI verify failed: test/postgres-engine-config-cache.test.ts mutated
process.env.GBRAIN_CONFIG_CACHE_TTL_MS directly in beforeEach/afterEach.
Wrap each test body in withEnv() (test/helpers/with-env.ts) instead.

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

src/commands/autopilot-fanout.ts

@@ -186,18 +186,6 @@ 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

@@ -901,27 +901,13 @@ 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 ||
-          staleCycleSources > 0;
+          score < 70;
 
-        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN && staleCycleSources === 0;
+        const shouldSleep = score >= 95 && plan.length === 0 && minutesSinceLastFull < FULL_CYCLE_FLOOR_MIN;
 
         if (shouldSleep) {
           if (jsonMode) {

src/core/cycle.ts

@@ -854,10 +854,7 @@ 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) 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).
+ * to pre-v0.18 global config.sync.* keys).
  */
 async function resolveSourceForDir(
   engine: BrainEngine,
@@ -868,10 +865,10 @@ 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 2`,
+      `SELECT id FROM sources WHERE local_path = $1 LIMIT 1`,
       [brainDir],
     );
-    return rows.length === 1 ? rows[0]!.id : undefined;
+    return rows[0]?.id;
   } catch {
     // sources table might not exist on very old brains — fall through.
     return undefined;
@@ -2368,23 +2365,17 @@ export async function runCycle(
   }
 
   // v0.38 (codex r1 P0-5): persist per-source cycle completion timestamp
-  // 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)
+  // 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)
   //   - 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 (cycleSourceId && engine && !dryRun && !aborted && (status === 'ok' || status === 'clean' || status === 'partial')) {
+  if (opts.sourceId && 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
@@ -2394,13 +2385,13 @@ 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(cycleSourceId, {
+      await engine.updateSourceConfig(opts.sourceId, {
         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 ${cycleSourceId}: ${e instanceof Error ? e.message : String(e)}`);
+      console.warn(`[cycle] failed to write last_source_cycle_at for source ${opts.sourceId}: ${e instanceof Error ? e.message : String(e)}`);
     }
   }
 

src/core/postgres-engine.ts

@@ -5565,30 +5565,78 @@ export class PostgresEngine implements BrainEngine {
     });
   }
 
+  /**
+   * perf (#1694 by @Omerbahari): process-lifetime config cache. A single
+   * search fires ~85 getConfig() reads (loadConfigWithEngine x2, plus
+   * mode/cache/intent/rerank/graph-signals resolvers). On a remote pooler
+   * each read is a round-trip; serial they dominate query latency and can
+   * push the op handler past cli.ts's 10s disconnect force-exit, truncating
+   * stdout. First read batch-loads the whole `config` table into this Map
+   * (inside the same connRetry posture as the per-key read — #1603/#1891);
+   * setConfig/unsetConfig write through. TTL bounds staleness for
+   * multi-writer processes; GBRAIN_CONFIG_CACHE_TTL_MS=0 disables.
+   * Only present keys are stored — Map.has() distinguishes known-absent.
+   */
+  private _configCache: Map<string, string> | null = null;
+  private _configCacheLoadedAt = 0;
+  private _configCacheLoad: Promise<void> | null = null;
+  private get _configCacheTtlMs(): number {
+    const raw = process.env.GBRAIN_CONFIG_CACHE_TTL_MS;
+    if (raw !== undefined) {
+      const n = parseInt(raw, 10);
+      if (Number.isFinite(n) && n >= 0) return n;
+    }
+    return 30_000;
+  }
+
   async getConfig(key: string): Promise<string | null> {
     // #1603: a transient pooler drop on this read used to throw / fall through
     // to defaults silently — which on remote Postgres surfaces as the wrong
-    // search mode/knobs and empty-stdout queries.
-    return this.connRetry(async () => {
-      const rows = await this.sql`SELECT value FROM config WHERE key = ${key}`;
-      return rows.length > 0 ? (rows[0].value as string) : null;
-    });
+    // search mode/knobs and empty-stdout queries. Both the batch load and the
+    // cache-off per-key read keep the connRetry reconnect posture.
+    const ttl = this._configCacheTtlMs;
+    if (ttl === 0) {
+      return this.connRetry(async () => {
+        const rows = await this.sql`SELECT value FROM config WHERE key = ${key}`;
+        return rows.length > 0 ? (rows[0].value as string) : null;
+      });
+    }
+    if (this._configCache === null || Date.now() - this._configCacheLoadedAt >= ttl) {
+      // Single-flight: concurrent cold reads share one batch load.
+      this._configCacheLoad ??= this.connRetry(async () => {
+        const rows = await this.sql`SELECT key, value FROM config` as unknown as
+          Array<{ key: string; value: string | null }>;
+        const map = new Map<string, string>();
+        for (const r of rows) if (r.value != null) map.set(r.key, r.value);
+        this._configCache = map;
+        this._configCacheLoadedAt = Date.now();
+      }).finally(() => {
+        this._configCacheLoad = null;
+      });
+      await this._configCacheLoad;
+    }
+    return this._configCache!.has(key) ? this._configCache!.get(key)! : null;
   }
 
   async setConfig(key: string, value: string): Promise<void> {
-    return this.connRetry(async () => {
+    await this.connRetry(async () => {
       await this.sql`
         INSERT INTO config (key, value) VALUES (${key}, ${value})
         ON CONFLICT (key) DO UPDATE SET value = EXCLUDED.value
       `;
     });
+    // Write-through so a long-lived process never serves stale config.
+    this._configCache?.set(key, value);
   }
 
   async unsetConfig(key: string): Promise<number> {
-    return this.connRetry(async () => {
+    const count = await this.connRetry(async () => {
       const result = await this.sql`DELETE FROM config WHERE key = ${key}` as unknown as { count: number };
       return result.count ?? 0;
     });
+    // Write-through: known-absent, so the cache doesn't serve a stale value.
+    this._configCache?.delete(key);
+    return count;
   }
 
   async listConfigKeys(prefix: string): Promise<string[]> {

test/autopilot-fanout-wiring.test.ts

@@ -54,20 +54,6 @@ 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

@@ -14,7 +14,6 @@ import { describe, test, expect } from 'bun:test';
 import {
   readLastFullCycleAt,
   isSourceStale,
-  countStaleSources,
   selectSourcesForDispatch,
   resolveFanoutMax,
   dispatchPerSource,
@@ -75,23 +74,6 @@ 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

@@ -3,10 +3,8 @@
  * cycles. Closes codex round-1 P0-5 (write site for last_full_cycle_at
  * was unspecified pre-PR).
  *
- * 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)
+ * Conditions for write:
+ *   - opts.sourceId is set (legacy callers without sourceId skip the write)
  *   - engine is non-null (no-DB path skips)
  *   - status is 'ok' | 'clean' | 'partial' (failed/skipped don't mark fresh)
  *   - dryRun is false
@@ -92,45 +90,17 @@ describe('runCycle last_full_cycle_at exit hook', () => {
     });
   });
 
-  test('no explicit sourceId but brainDir resolves a source → writes the resolved source timestamp', async () => {
+  test('legacy caller (no sourceId) does NOT write any source timestamp', async () => {
     await withEnv({ GBRAIN_HOME: gbrainHome }, async () => {
-      // 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 seedSource('default-like');
+      // No sourceId passed; should remain untouched.
       await runCycle(engine, {
         brainDir,
         phases: ['lint'],
       });
-      expect(await readLastFullCycleAt('unmatched')).toBeNull();
+      // No per-source write happens; default source's config stays empty.
+      const after = await readLastFullCycleAt('default-like');
+      expect(after).toBeNull();
     });
   });
 

test/e2e/helpers.ts

@@ -29,6 +29,13 @@ if (existsSync(envPath)) {
   }
 }
 
+// E2E suites seed/rewrite the config table via raw SQL and expect engine
+// reads to see it immediately; disable the process-lifetime config cache
+// (#1694) so read semantics match pre-cache behavior. Spawned CLI
+// subprocesses inherit this. Cache semantics are pinned by
+// test/postgres-engine-config-cache.test.ts.
+process.env.GBRAIN_CONFIG_CACHE_TTL_MS ??= '0';
+
 const DATABASE_URL = process.env.DATABASE_URL;
 const FIXTURES_DIR = resolve(import.meta.dir, 'fixtures');
 

test/postgres-engine-config-cache.test.ts

@@ -0,0 +1,112 @@
+/**
+ * Process-lifetime config cache (#1694 takeover, by @Omerbahari).
+ *
+ * A single search fires ~85 getConfig() reads; on a remote pooler each is a
+ * round-trip. The first read now batch-loads the whole `config` table into a
+ * Map; setConfig/unsetConfig write through; TTL bounds multi-writer
+ * staleness; GBRAIN_CONFIG_CACHE_TTL_MS=0 restores per-key reads.
+ *
+ * Pure: stubs `_sql` with a call-counting fake; no real DB.
+ */
+
+import { describe, it, expect } from 'bun:test';
+import { PostgresEngine } from '../src/core/postgres-engine.ts';
+import { withEnv } from './helpers/with-env.ts';
+
+const FAST_RETRY = { maxRetries: 3, delayMs: 1, delayMaxMs: 1, jitter: 'none' as const };
+
+/** Engine whose `sql` records every query's template strings and returns `rows`. */
+function makeEngine(rows: unknown[]) {
+  const e = new PostgresEngine();
+  const calls: string[] = [];
+  (e as unknown as { _connectionStyle: string })._connectionStyle = 'instance';
+  (e as unknown as { _bulkRetryOptsCache: unknown })._bulkRetryOptsCache = FAST_RETRY;
+  (e as unknown as { _sql: unknown })._sql = (strings: TemplateStringsArray) => {
+    calls.push(strings.join('?'));
+    return Promise.resolve(rows);
+  };
+  return { engine: e, calls };
+}
+
+/** Run `fn` with GBRAIN_CONFIG_CACHE_TTL_MS set (or cleared when undefined). */
+const withTtl = (ttl: string | undefined, fn: () => Promise<void>) =>
+  withEnv({ GBRAIN_CONFIG_CACHE_TTL_MS: ttl }, fn);
+
+describe('PostgresEngine config cache (#1694)', () => {
+  it('batch-loads once and serves repeat reads from the cache', () => withTtl(undefined, async () => {
+    const { engine, calls } = makeEngine([
+      { key: 'search.mode', value: 'balanced' },
+      { key: 'embedding_multimodal', value: 'true' },
+    ]);
+    expect(await engine.getConfig('search.mode')).toBe('balanced');
+    expect(await engine.getConfig('embedding_multimodal')).toBe('true');
+    expect(await engine.getConfig('search.mode')).toBe('balanced');
+    // One SELECT total — this is the whole point of the fix.
+    expect(calls.length).toBe(1);
+    expect(calls[0]).toContain('SELECT key, value FROM config');
+  }));
+
+  it('returns null for a known-absent key without an extra round-trip', () => withTtl(undefined, async () => {
+    const { engine, calls } = makeEngine([{ key: 'a', value: '1' }]);
+    expect(await engine.getConfig('missing.key')).toBeNull();
+    expect(await engine.getConfig('missing.key')).toBeNull();
+    expect(calls.length).toBe(1);
+  }));
+
+  it('setConfig writes through so subsequent reads see the new value', () => withTtl(undefined, async () => {
+    const { engine, calls } = makeEngine([{ key: 'k', value: 'old' }]);
+    expect(await engine.getConfig('k')).toBe('old');
+    await engine.setConfig('k', 'new');
+    expect(await engine.getConfig('k')).toBe('new');
+    expect(calls.length).toBe(2); // batch load + upsert; no re-read
+  }));
+
+  it('unsetConfig writes through so subsequent reads see absence', () => withTtl(undefined, async () => {
+    const { engine } = makeEngine([{ key: 'k', value: 'v' }]);
+    expect(await engine.getConfig('k')).toBe('v');
+    await engine.unsetConfig('k');
+    expect(await engine.getConfig('k')).toBeNull();
+  }));
+
+  it('concurrent cold reads share a single batch load (single-flight)', () => withTtl(undefined, async () => {
+    const { engine, calls } = makeEngine([{ key: 'k', value: 'v' }]);
+    const [a, b, c] = await Promise.all([
+      engine.getConfig('k'),
+      engine.getConfig('k'),
+      engine.getConfig('other'),
+    ]);
+    expect([a, b, c]).toEqual(['v', 'v', null]);
+    expect(calls.length).toBe(1);
+  }));
+
+  it('GBRAIN_CONFIG_CACHE_TTL_MS=0 disables the cache (per-key reads)', () => withTtl('0', async () => {
+    const { engine, calls } = makeEngine([{ value: 'v' }]);
+    expect(await engine.getConfig('k')).toBe('v');
+    expect(await engine.getConfig('k')).toBe('v');
+    expect(calls.length).toBe(2);
+    expect(calls[0]).toContain('SELECT value FROM config WHERE key =');
+  }));
+
+  it('an expired TTL reloads from the database', () => withTtl('1', async () => {
+    const { engine, calls } = makeEngine([{ key: 'k', value: 'v' }]);
+    expect(await engine.getConfig('k')).toBe('v');
+    await new Promise((r) => setTimeout(r, 5));
+    expect(await engine.getConfig('k')).toBe('v');
+    expect(calls.length).toBe(2); // two batch loads
+  }));
+
+  it('the batch load keeps the connRetry reconnect posture (#1603/#1891)', () => withTtl(undefined, async () => {
+    const e = new PostgresEngine();
+    (e as unknown as { _connectionStyle: string })._connectionStyle = 'instance';
+    (e as unknown as { _sql: unknown })._sql = null; // torn-down pool → retryable
+    (e as unknown as { _bulkRetryOptsCache: unknown })._bulkRetryOptsCache = FAST_RETRY;
+    let reconnects = 0;
+    (e as unknown as { reconnect: () => Promise<void> }).reconnect = async () => {
+      reconnects++;
+      (e as unknown as { _sql: unknown })._sql = () =>
+        Promise.resolve([{ key: 'k', value: 'v' }]);
+    };
+    expect(await e.getConfig('k')).toBe('v');
+    expect(reconnects).toBe(1);
+  }));
+});

test/postgres-engine-config-reconnect.test.ts

@@ -43,7 +43,9 @@ function makeTornDownEngine(poolResult: unknown): { engine: PostgresEngine; reco
 
 describe('PostgresEngine non-batch config accessors self-heal (PR #1891 takeover)', () => {
   it('getConfig reconnects + retries a null instance pool, then returns the value', async () => {
-    const { engine, reconnects } = makeTornDownEngine([{ value: 'live-value' }]);
+    // Rows carry `key` too: getConfig's default cached path batch-loads
+    // `SELECT key, value FROM config` (#1694) through the same connRetry.
+    const { engine, reconnects } = makeTornDownEngine([{ key: 'some.key', value: 'live-value' }]);
     expect(await engine.getConfig('some.key')).toBe('live-value');
     expect(reconnects()).toBe(1); // exactly one reconnect closed the gap
   });