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/extract.ts

@@ -43,7 +43,7 @@ import {
 } from '../core/link-extraction.ts';
 import { createProgress } from '../core/progress.ts';
 import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts';
-import { pathToSlug, slugifyPath, pruneDir, isSyncable } from '../core/sync.ts';
+import { pathToSlug, pruneDir, isSyncable } from '../core/sync.ts';
 // v0.41.18.0: withRetry + isRetryableConnError + WithRetryOpts moved to
 // src/core/retry.ts as the canonical primitive. Engine methods
 // (addLinksBatch/addTimelineEntriesBatch/upsertChunks) now self-retry via
@@ -269,24 +269,14 @@ export function extractMarkdownLinks(content: string): { name: string; relTarget
 export function resolveSlug(fileDir: string, relTarget: string, allSlugs: Set<string>): string | null {
   const targetNoExt = relTarget.endsWith('.md') ? relTarget.slice(0, -3) : relTarget;
 
-  // Issue #1964: wikilinks carry raw Obsidian paths (`[[llm-wiki/entities/AI 3.0]]`)
-  // but allSlugs holds sync-slugified slugs (`llm-wiki/entities/ai-3.0`). Try the
-  // raw candidate first (back-compat), then the sync-consistent slugified form.
-  const hit = (candidate: string): string | null => {
-    if (allSlugs.has(candidate)) return candidate;
-    const slugified = slugifyPath(candidate);
-    if (slugified !== candidate && allSlugs.has(slugified)) return slugified;
-    return null;
-  };
-
-  const s1 = hit(join(fileDir, targetNoExt));
-  if (s1) return s1;
+  const s1 = join(fileDir, targetNoExt);
+  if (allSlugs.has(s1)) return s1;
 
   const parts = fileDir.split('/').filter(Boolean);
   for (let strip = 1; strip <= parts.length; strip++) {
     const ancestor = parts.slice(0, parts.length - strip).join('/');
-    const candidate = hit(ancestor ? join(ancestor, targetNoExt) : targetNoExt);
-    if (candidate) return candidate;
+    const candidate = ancestor ? join(ancestor, targetNoExt) : targetNoExt;
+    if (allSlugs.has(candidate)) return candidate;
   }
 
   return null;

src/core/link-extraction.ts

@@ -14,7 +14,6 @@
 import type { BrainEngine } from './engine.ts';
 import type { PageType } from './types.ts';
 import { ensureWellFormed } from './text-safe.ts';
-import { slugifyPath } from './sync.ts';
 
 /**
  * v0.42.7 — link-extraction version stamp. Bump this ISO timestamp whenever the
@@ -483,29 +482,14 @@ export async function extractPageLinks(
     // pre-v0.40.8.2 behavior of dropping bare wikilinks outside
     // DIR_PATTERN.
     if (ref.needsResolution) {
-      if (typeof resolver.resolveBasenameMatches !== 'function') continue;
+      if (!opts.globalBasename || typeof resolver.resolveBasenameMatches !== 'function') {
+        continue;
+      }
       // Issue #972 (codex): resolve by the wikilink TARGET (ref.slug — the
       // text inside `[[...]]` before any `|`), NOT the display alias
       // (ref.name = match[2]). `[[struktura|the project]]` must resolve
       // `struktura`, not "the project". The display text is for context only.
-      //
-      // Issue #1964: a dir-qualified wikilink (`[[llm-wiki/entities/AI 3.0]]`)
-      // carries a raw Obsidian path while page slugs are sync-slugified
-      // (`llm-wiki/entities/ai-3.0`). Slugify the path the same way sync does,
-      // then match by exact slug or path-suffix (wiki-root-relative authoring).
-      // This runs regardless of global_basename — it's dir-qualified, so the
-      // cross-dir false-positive risk the flag guards against doesn't apply.
-      // Mirrors the FS path's resolveSlug ancestor walk. Bare `[[name]]`
-      // wikilinks still require the global_basename flag.
-      let matches: string[] = [];
-      const slugified = ref.slug.includes('/') ? slugifyPath(ref.slug) : '';
-      if (slugified.includes('/')) {
-        const tail = slugified.slice(slugified.lastIndexOf('/') + 1);
-        matches = (await resolver.resolveBasenameMatches(tail))
-          .filter(m => m === slugified || m.endsWith(`/${slugified}`));
-      } else if (opts.globalBasename) {
-        matches = await resolver.resolveBasenameMatches(ref.slug);
-      }
+      const matches = await resolver.resolveBasenameMatches(ref.slug);
       if (matches.length === 0) continue;
       const idx = content.indexOf(ref.slug);
       const context = idx >= 0 ? excerpt(content, idx, 240) : ref.name;

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/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/extract-fs.test.ts

@@ -389,33 +389,6 @@ describe('resolveSlugAll', () => {
   });
 });
 
-// ─── issue #1964: cross-directory wikilinks — slug/path mismatch ──────────
-
-describe('issue #1964: raw Obsidian wikilink paths resolve to sync-slugified slugs', () => {
-  test('resolveSlug slugifies the candidate (sync-consistent), no flag needed', () => {
-    const all = new Set(['llm-wiki/entities/ai-3.0']);
-    // Wikilink literal `[[llm-wiki/entities/AI 3.0]]` — spaces + uppercase.
-    expect(resolveSlug('llm-wiki/notes', 'llm-wiki/entities/AI 3.0.md', all))
-      .toBe('llm-wiki/entities/ai-3.0');
-  });
-
-  test('resolveSlug slugifies raw (unslugified) fileDir too', () => {
-    const all = new Set(['llm-wiki/entities/ai-3.0']);
-    // fileDir comes from dirname(relPath) — the raw on-disk directory.
-    expect(resolveSlug('LLM Wiki/Notes', 'entities/AI 3.0.md', all))
-      .toBe('llm-wiki/entities/ai-3.0');
-  });
-
-  test('extractLinksFromFile resolves cross-directory wikilink with flag OFF as a typed edge', async () => {
-    const allSlugs = new Set(['llm-wiki/entities/ai-3.0', 'llm-wiki/notes/roadmap']);
-    const content = '---\ntitle: Roadmap\ntype: concept\n---\n\nSee [[llm-wiki/entities/AI 3.0]].\n';
-    const links = await extractLinksFromFile(content, 'llm-wiki/notes/roadmap.md', allSlugs);
-    expect(links.map(l => l.to_slug)).toEqual(['llm-wiki/entities/ai-3.0']);
-    // Dir-qualified path resolution is exact, NOT the basename fallback.
-    expect(links[0].link_type).not.toBe('wikilink_basename');
-  });
-});
-
 describe('issue #972 repro: bare wikilinks resolve when flag is on', () => {
   // End-to-end: reproduces the issue's exact repro inside a tempdir +
   // PGLite, then asserts edge count under both flag states.

test/link-extraction.test.ts

@@ -9,8 +9,6 @@ import {
   parseTimelineEntries,
   isAutoLinkEnabled,
   FRONTMATTER_LINK_MAP,
-  buildBasenameIndex,
-  queryBasenameIndex,
   type SlugResolver,
 } from '../src/core/link-extraction.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
@@ -426,46 +424,6 @@ describe('extractPageLinks', () => {
     expect(strk!.linkType).toBe('wikilink_basename');
   });
 
-  // ─── issue #1964: dir-qualified wikilinks with raw Obsidian paths ────────
-
-  test('#1964: dir-qualified wikilink resolves via sync-consistent slugification (flag OFF)', async () => {
-    // `[[llm-wiki/entities/AI 3.0]]` is a raw Obsidian path; the page slug
-    // is the sync-slugified `llm-wiki/entities/ai-3.0`. Must resolve WITHOUT
-    // global_basename (it's dir-qualified) and must NOT leak to a same-tail
-    // page in a different directory.
-    const resolver: SlugResolver = {
-      resolve: async () => null,
-      resolveBasenameMatches: async (name) =>
-        name === 'ai-3.0' ? ['other/ai-3.0', 'llm-wiki/entities/ai-3.0'] : [],
-    };
-    const { candidates } = await extractPageLinks(
-      'llm-wiki/notes/roadmap',
-      'See [[llm-wiki/entities/AI 3.0]] for the model.',
-      {}, 'concept', resolver,
-      // opts.globalBasename omitted (= false) — path is dir-qualified
-    );
-    expect(candidates.map(c => c.targetSlug)).toEqual(['llm-wiki/entities/ai-3.0']);
-    expect(candidates[0].linkType).toBe('wikilink_basename');
-    expect(candidates[0].linkSource).toBe('wikilink-resolved');
-  });
-
-  test('#1964: path-suffix match resolves wiki-root-relative paths against a real index', async () => {
-    // Author writes `[[llm-wiki/entities/AI 3.0]]` but the brain nests the
-    // wiki under a vault dir. Suffix match rescues it; queried through the
-    // REAL basename index so the tail-key lookup is exercised end to end.
-    const idx = buildBasenameIndex(['vault/llm-wiki/entities/ai-3.0', 'people/ai-3.0']);
-    const resolver: SlugResolver = {
-      resolve: async () => null,
-      resolveBasenameMatches: async (name) => queryBasenameIndex(idx, name),
-    };
-    const { candidates } = await extractPageLinks(
-      'vault/llm-wiki/notes/roadmap',
-      'See [[llm-wiki/entities/AI 3.0]].',
-      {}, 'concept', resolver,
-    );
-    expect(candidates.map(c => c.targetSlug)).toEqual(['vault/llm-wiki/entities/ai-3.0']);
-  });
-
   test('opts.skipFrontmatter suppresses the frontmatter pass', async () => {
     // Real resolver shape that WOULD resolve frontmatter source: too,
     // but skipFrontmatter blocks the path entirely.

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
   });