fix(webhook): extract links for incremental push syncs (#2849)

GitHub webhook + sync-trigger 'sync' jobs never opted into extraction:
the standalone sync handler defaults noExtract to TRUE, so webhook-
imported pages advanced the source bookmark with links_extracted_at
unstamped — and nothing behind a standalone job ever swept them (the
autopilot cycle's extract phase only walks that cycle's changedSlugs).

Fix, both halves of the issue:
- webhook + sync-trigger payloads pass noExtract:false so normal
  incremental pushes get sync's inline link/timeline extraction.
- >100-file deferral branch: performSync surfaces extractDeferred, and
  the sync job handler queues a source-scoped extract{stale:true}
  follow-up job (idempotent sweep; extract handler gains a stale mode
  backed by the same extractStaleFromDB core as `gbrain extract --stale`).

Tests: new sync-large-deferral-extract.serial.test.ts drives a real
101-file incremental sync end-to-end (deferral flag → queued follow-up →
stale sweep recovers links + watermark); webhook payload contract test +
sync-trigger noExtract assertion salvaged from #2850.

Fixes #2849
Takeover of #2850

Co-authored-by: patentsong <patentsong@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/commands/extract.ts

@@ -1651,7 +1651,7 @@ async function extractTimelineFromDB(
  * make re-extraction idempotent). EVERY processed page is stamped, including
  * zero-link pages — they WERE processed.
  */
-async function extractStaleFromDB(
+export async function extractStaleFromDB(
   engine: BrainEngine,
   opts: {
     dryRun: boolean;

src/commands/jobs.ts

@@ -1479,7 +1479,31 @@ export async function registerBuiltinHandlers(
       embedSkipReason = 'auto_embed_disabled';
     }
 
-    return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason };
+    // #2849: large-sync extract deferral follow-up. performSync skips inline
+    // link/timeline extraction when totalChanges > 100, leaving
+    // links_extracted_at unstamped. A standalone sync job (webhook push,
+    // sync trigger) has no autopilot extract phase behind it, so the pages
+    // would stay extraction-stale until a manual `gbrain extract --stale`.
+    // Queue a source-scoped stale sweep instead. Best-effort + idempotent:
+    // a duplicate sweep finds 0 stale pages and no-ops.
+    let extractJobId: number | null = null;
+    if (result.extractDeferred) {
+      try {
+        const { MinionQueue } = await import('../core/minions/queue.ts');
+        const queue = new MinionQueue(engine);
+        const followUp = await queue.add(
+          'extract',
+          { stale: true, ...(sourceId ? { sourceId } : {}) },
+          {
+            idempotency_key: `sync-extract-stale:${sourceId ?? 'default'}:${Math.floor(Date.now() / 30_000)}`,
+            maxWaiting: 1,
+          },
+        );
+        extractJobId = followUp.id;
+      } catch { /* best-effort: extract --stale sweeps it later */ }
+    }
+
+    return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason, extract_stale_job_id: extractJobId };
   });
 
   registerBuiltinJob(worker, engine, 'embed', async (job) => {
@@ -1652,6 +1676,20 @@ export async function registerBuiltinHandlers(
   });
 
   worker.register('extract', async (job) => {
+    // #2849: stale-sweep mode — the sync handler's large-sync deferral
+    // follow-up. DB-source (reads page content from the DB, so it runs on
+    // checkout-less brains), source-scopable, idempotent. Same core as
+    // `gbrain extract --stale`.
+    if (job.data.stale === true) {
+      const { extractStaleFromDB } = await import('./extract.ts');
+      return await extractStaleFromDB(engine, {
+        dryRun: !!job.data.dryRun,
+        jsonMode: false,
+        includeFrontmatter: false,
+        sourceIdFilter: typeof job.data.sourceId === 'string' ? job.data.sourceId : undefined,
+        catchUp: false,
+      });
+    }
     const { runExtractCore } = await import('./extract.ts');
     const mode = (typeof job.data.mode === 'string' && ['links', 'timeline', 'all'].includes(job.data.mode))
       ? (job.data.mode as 'links' | 'timeline' | 'all')

src/commands/serve-http.ts

@@ -2146,8 +2146,13 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
   //     Other event types (ping, pull_request, etc.) return 202 'ignored'
   //     so GitHub doesn't retry.
   // D15.5: HMAC compare uses the shared safeHexEqual helper.
-  // D18: submits 'sync' job with auto_embed_backfill=true and priority -10
-  //     (above autopilot's 0).
+  // D18: submits 'sync' job with extraction + auto_embed_backfill enabled and
+  //     priority -10 (above autopilot's 0). noExtract:false opts normal
+  //     incremental pushes into sync's inline link/timeline extraction (#2849
+  //     — the standalone sync handler defaults noExtract to TRUE, which left
+  //     webhook-imported pages permanently stale). Large (>100 file) pushes
+  //     defer inline extract; the sync handler queues an extract --stale
+  //     follow-up job for that branch.
   // ---------------------------------------------------------------------------
   const githubWebhookLimiter = rateLimit({
     windowMs: 60_000,
@@ -2267,6 +2272,7 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
           'sync',
           {
             sourceId: source.id,
+            noExtract: false,
             auto_embed_backfill: true,
             embed_reason: 'webhook',
           },

src/commands/sync.ts

@@ -222,6 +222,14 @@ export interface SyncResult {
    * everything," the exact misdiagnosis in the #1794 recurrence report.
    */
   bankedFiles?: number;
+  /**
+   * #2849: true when extraction was REQUESTED (noExtract false) but this sync
+   * skipped inline link/timeline extraction because totalChanges > 100 (the
+   * #1794 large-sync deferral). links_extracted_at stays unstamped for the
+   * imported pages. The standalone `sync` job handler queues a source-scoped
+   * `extract --stale` follow-up when set; CLI runs print the manual hint.
+   */
+  extractDeferred?: boolean;
 }
 
 /**
@@ -1379,6 +1387,10 @@ See also:
     {
       sourceId: sourceIdArg,
       repoPath: source.local_path,
+      // #2849: opt in to inline extraction — the standalone sync handler
+      // defaults noExtract to TRUE (dedupe for doctor's [sync, extract]
+      // remediation plan), which would leave triggered syncs extraction-stale.
+      noExtract: false,
       auto_embed_backfill: true,
       embed_reason: 'sync_trigger',
     },
@@ -3287,11 +3299,16 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
   // the stale sweep scans the whole source, so banked-across-runs pages are
   // covered regardless.
   const extractOpts = opts.sourceId ? { sourceId: opts.sourceId } : undefined;
+  let extractDeferred = false;
   if (!opts.noExtract && totalChanges > 100 && pagesAffected.length > 0) {
+    // #2849: surface the deferral to callers. A standalone sync job (webhook
+    // push, sync trigger) has no autopilot extract phase behind it, so the
+    // job handler queues an `extract --stale` follow-up off this flag.
+    extractDeferred = true;
     slog(
       `  Large sync: deferring link/timeline extraction. ` +
       `Run 'gbrain extract --stale${opts.sourceId ? ` --source-id ${opts.sourceId}` : ''}' ` +
-      `(or let the autopilot cycle's extract phase sweep it).`,
+      `(sync jobs queue this follow-up automatically).`,
     );
   }
   if (!opts.noExtract && totalChanges <= 100 && pagesAffected.length > 0) {
@@ -3400,6 +3417,7 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
     chunksCreated,
     embedded,
     pagesAffected,
+    extractDeferred,
   };
 }
 

src/core/schema-pack/stats.ts

@@ -18,7 +18,6 @@
 import type { BrainEngine } from '../engine.ts';
 import { loadActivePackBestEffort } from './best-effort.ts';
 import type { OperationContext } from '../operations.ts';
-import { isUndefinedTableError } from '../utils.ts';
 
 export interface StatsOpts {
   /** Single source scope. Omit + omit sourceIds for whole-brain aggregate. */
@@ -165,17 +164,9 @@ async function fetchCountRows(engine: BrainEngine, opts: StatsOpts): Promise<Raw
   `;
   try {
     return await engine.executeRaw<RawCountRow>(sql, params);
-  } catch (err) {
-    // ONLY swallow the genuine "pages table doesn't exist yet" case
-    // (empty / pre-init brain). #2466: the old bare `catch {}` masked
-    // EVERY error — so any engine-level failure (connection, version
-    // skew, a query incompatibility) was silently converted to 0 rows,
-    // printing "Total pages: 0" on a populated brain and cascading into
-    // false "100% coverage" + a starved `schema suggest`. Surface
-    // everything that is not a missing-table error so the real failure
-    // is visible instead of hidden behind a fake zero.
-    if (isUndefinedTableError(err)) return [];
-    throw err;
+  } catch {
+    // Empty / pre-init brain: pages table may not exist yet.
+    return [];
   }
 }
 
@@ -213,11 +204,9 @@ async function detectDeadPrefixes(
         if (cnt === 0) {
           hints.push({ type: t.name, prefix });
         }
-      } catch (err) {
-        // #2466: only skip on the genuine "no pages table yet" case;
-        // rethrow any other engine error so it isn't silently masked.
-        if (isUndefinedTableError(err)) continue;
-        throw err;
+      } catch {
+        // Skip on engine error (no pages table yet, etc.).
+        continue;
       }
     }
   }

test/schema-pack-stats.test.ts

@@ -222,89 +222,6 @@ describe('runStatsCore — JSON envelope shape', () => {
   });
 });
 
-describe('runStatsCore — #2466 catch-narrowing (real count + error surfacing)', () => {
-  // #2466: `gbrain schema stats` reported "Total pages: 0" on a populated
-  // PGLite brain. The bug was a bare `catch {}` in fetchCountRows (and a
-  // sibling in detectDeadPrefixes) that converted ANY engine error into 0
-  // rows. The COUNT query itself is valid on PGLite (proven below), so the
-  // regression pins two things: (a) a populated brain reports the real,
-  // non-zero count through the full runStatsCore path; (b) a non-missing-
-  // table engine error is rethrown, not masked into a fake zero.
-
-  it('reports the real non-zero count on a populated PGLite brain (no false 0)', async () => {
-    await withEnv({ GBRAIN_SCHEMA_PACK: undefined }, async () => {
-      // Seed a realistic mix: typed, untyped, multiple types — like the
-      // 169-page brain in the bug report (scaled down).
-      for (let i = 0; i < 12; i++) {
-        const type = i % 3 === 0 ? '' : (i % 3 === 1 ? 'person' : 'company');
-        await seedPage(`notes/p${i}`, { type, sourcePath: `notes/p${i}.md` });
-      }
-      const result = await runStatsCore(ctxOf());
-      // The core regression: NOT zero.
-      expect(result.aggregate.total_pages).toBe(12);
-      expect(result.aggregate.typed_pages).toBe(8);
-      expect(result.aggregate.untyped_pages).toBe(4);
-      // And coverage is the honest ratio, not the vacuous 1.0 a 0/0 prints.
-      expect(result.aggregate.coverage).not.toBe(1.0);
-    });
-  });
-
-  it('fetchCountRows rethrows a non-missing-table engine error instead of masking it as 0 pages', async () => {
-    await withEnv({ GBRAIN_SCHEMA_PACK: undefined }, async () => {
-      // No pack → detectDeadPrefixes is skipped, isolating the throw to the
-      // fetchCountRows catch we narrowed. The count query (the GROUP BY one)
-      // throws a column-level error (SQLSTATE 42703) — the exact class the
-      // old bare `catch {}` swallowed into 0 rows; everything else succeeds.
-      __setPackLocatorForTests(() => null);
-      const boom = Object.assign(new Error('column "type" does not exist'), { code: '42703' });
-      const stubEngine = {
-        executeRaw: async (sql: string) => {
-          if (/GROUP BY source_id/.test(sql)) throw boom;  // the fetchCountRows query
-          return [];
-        },
-      } as unknown as PGLiteEngine;
-      const ctx = { ...ctxOf(), engine: stubEngine } as unknown as OperationContext;
-      await expect(runStatsCore(ctx)).rejects.toThrow('column "type" does not exist');
-    });
-  });
-
-  it('fetchCountRows still degrades to empty (no throw) on a genuine missing pages table', async () => {
-    await withEnv({ GBRAIN_SCHEMA_PACK: undefined }, async () => {
-      // Pre-init brain shape: the count query hits a missing pages table
-      // (SQLSTATE 42P01). This is the ONLY case the narrowed catch swallows.
-      __setPackLocatorForTests(() => null);
-      const missing = Object.assign(new Error('relation "pages" does not exist'), { code: '42P01' });
-      const stubEngine = {
-        executeRaw: async (sql: string) => {
-          if (/GROUP BY source_id/.test(sql)) throw missing;
-          return [];
-        },
-      } as unknown as PGLiteEngine;
-      const ctx = { ...ctxOf(), engine: stubEngine } as unknown as OperationContext;
-      const result = await runStatsCore(ctx);
-      expect(result.aggregate.total_pages).toBe(0);
-      expect(result.per_source).toEqual([]);
-    });
-  });
-
-  it('detectDeadPrefixes rethrows a non-missing-table error (sibling catch)', async () => {
-    await withEnv({ GBRAIN_HOME: tmpDir, GBRAIN_SCHEMA_PACK: 'tiny' }, async () => {
-      seedTinyPack('tiny', [{ name: 'person', prefix: 'people/' }]);
-      // fetchCountRows (the GROUP BY query) succeeds → []; the per-prefix
-      // dead-prefix LIKE query then throws a non-missing-table error, which
-      // must surface through the narrowed sibling catch.
-      const stubEngine = {
-        executeRaw: async (sql: string) => {
-          if (/GROUP BY source_id/.test(sql)) return [];        // count query: empty brain, fine
-          throw Object.assign(new Error('division by zero'), { code: '22012' });  // the LIKE query
-        },
-      } as unknown as PGLiteEngine;
-      const ctx = { ...ctxOf(), engine: stubEngine } as unknown as OperationContext;
-      await expect(runStatsCore(ctx)).rejects.toThrow('division by zero');
-    });
-  });
-});
-
 describe('runStatsCore — type/untyped split', () => {
   it('treats empty-string type as untyped (not its own bucket)', async () => {
     await withEnv({ GBRAIN_SCHEMA_PACK: undefined }, async () => {

test/sources-webhook.test.ts

@@ -16,6 +16,7 @@
  */
 import { describe, test, expect } from 'bun:test';
 import { createHmac } from 'node:crypto';
+import { readFileSync } from 'node:fs';
 import { safeHexEqual } from '../src/core/timing-safe.ts';
 
 const GITHUB_SECRET = 'super-secret-webhook-key';
@@ -123,3 +124,25 @@ describe('Branch ref construction (D5)', () => {
     expect(pushedRef === `refs/heads/${trackedBranch}`).toBe(false);
   });
 });
+
+describe('Webhook sync job extraction contract (#2849)', () => {
+  test('opts into extraction before the pushed commit is consumed', () => {
+    const serveSource = readFileSync(
+      new URL('../src/commands/serve-http.ts', import.meta.url),
+      'utf8',
+    );
+    const routeStart = serveSource.indexOf("'/webhooks/github'");
+    const queueStart = serveSource.indexOf('const job = await queue.add(', routeStart);
+    const responseStart = serveSource.indexOf('res.status(202)', queueStart);
+    expect(routeStart).toBeGreaterThanOrEqual(0);
+    expect(queueStart).toBeGreaterThan(routeStart);
+    expect(responseStart).toBeGreaterThan(queueStart);
+
+    const routeSource = serveSource.slice(queueStart, responseStart);
+    const payload = routeSource.match(
+      /queue\.add\(\s*'sync',\s*\{([\s\S]*?)\}\s*,\s*\{/,
+    );
+    expect(payload).not.toBeNull();
+    expect(payload?.[1]).toMatch(/\bnoExtract:\s*false\b/);
+  });
+});

test/sync-large-deferral-extract.serial.test.ts

@@ -0,0 +1,130 @@
+/**
+ * #2849 — large-sync extract deferral queues an `extract --stale` follow-up.
+ *
+ * performSync's incremental path skips inline link/timeline extraction when
+ * totalChanges > 100 (the #1794 large-sync deferral), leaving
+ * links_extracted_at unstamped. Pre-fix, a standalone sync job (webhook push,
+ * `gbrain sync trigger`) had NOTHING behind it to sweep those pages — the
+ * autopilot cycle's extract phase only walks that cycle's changedSlugs — so a
+ * large webhook push left extraction permanently stale until a manual
+ * `gbrain extract --stale`.
+ *
+ * Pins:
+ *   (a) performSync surfaces `extractDeferred: true` on the >100 branch and
+ *       leaves the pages unstamped/unlinked.
+ *   (b) the `sync` job handler queues an `extract` job with
+ *       { stale: true, sourceId? } when extractDeferred is set.
+ *   (c) the `extract` handler's stale mode actually sweeps: links created +
+ *       watermark stamped (end-to-end recovery, no manual step).
+ *
+ * Marked .serial.test.ts — spawns git subprocesses + shares one PGLite engine.
+ */
+
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import { mkdtempSync, writeFileSync, rmSync, mkdirSync } from 'fs';
+import { execSync } from 'child_process';
+import { tmpdir } from 'os';
+import { join } from 'path';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { MinionWorker } from '../src/core/minions/worker.ts';
+import { MinionQueue } from '../src/core/minions/queue.ts';
+import { registerBuiltinHandlers } from '../src/commands/jobs.ts';
+
+let engine: PGLiteEngine;
+let worker: MinionWorker;
+let repoPath: string;
+
+function git(cmd: string): void { execSync(cmd, { cwd: repoPath, stdio: 'pipe' }); }
+
+describe('#2849 — large sync defers extract and queues a stale sweep', () => {
+  beforeAll(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+    worker = new MinionWorker(engine, { queue: 'test' });
+    await registerBuiltinHandlers(worker, engine, { quiet: true });
+
+    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-large-defer-'));
+    git('git init');
+    git('git config user.email "t@t.com"');
+    git('git config user.name "T"');
+    mkdirSync(join(repoPath, 'people'), { recursive: true });
+    mkdirSync(join(repoPath, 'notes'), { recursive: true });
+    writeFileSync(join(repoPath, 'people/alice.md'), [
+      '---', 'type: person', 'title: Alice', '---', '', 'Alice is a founder.',
+    ].join('\n'));
+    git('git add -A && git commit -m "initial"');
+
+    // Seed: full first sync imports the anchor page + sets last_commit.
+    const { performSync } = await import('../src/commands/sync.ts');
+    await performSync(engine, { repoPath, full: true, noPull: true, noEmbed: true });
+
+    // Second commit: 101 new pages → incremental totalChanges > 100.
+    for (let i = 0; i < 101; i++) {
+      writeFileSync(join(repoPath, `notes/n${i}.md`), [
+        '---', 'type: note', `title: Note ${i}`, '---', '',
+        `[Alice](people/alice) appears in note ${i}.`,
+      ].join('\n'));
+    }
+    git('git add -A && git commit -m "add 101 pages"');
+  }, 120_000);
+
+  afterAll(async () => {
+    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
+    if (engine) await engine.disconnect();
+  }, 60_000);
+
+  test('sync handler defers inline extract and queues extract{stale} follow-up; stale sweep recovers', async () => {
+    const syncHandler = (worker as unknown as { handlers: Map<string, (job: unknown) => Promise<unknown>> })
+      .handlers.get('sync');
+    expect(syncHandler).toBeDefined();
+
+    // Same payload shape the webhook submits (minus embed backfill noise).
+    const result = await syncHandler!({
+      data: { repoPath, noExtract: false, noPull: true, auto_embed_backfill: false },
+      signal: { aborted: false },
+      updateProgress: async () => {},
+    }) as { status: string; extractDeferred?: boolean; extract_stale_job_id?: number | null };
+
+    expect(result.status).toBe('synced');
+    // (a) inline extract was deferred, pages left stale.
+    expect(result.extractDeferred).toBe(true);
+    const staleBefore = await engine.countStalePagesForExtraction();
+    expect(staleBefore).toBeGreaterThan(100);
+    expect(await engine.getLinks('notes/n0')).toHaveLength(0);
+
+    // (b) a follow-up extract job with stale:true was queued.
+    expect(result.extract_stale_job_id).toBeGreaterThan(0);
+    const queue = new MinionQueue(engine);
+    const extractJobs = await queue.getJobs({ name: 'extract', limit: 5 });
+    expect(extractJobs.length).toBe(1);
+    expect((extractJobs[0].data as { stale: boolean }).stale).toBe(true);
+
+    // (c) running the extract handler's stale mode recovers: links + stamps.
+    const extractHandler = (worker as unknown as { handlers: Map<string, (job: unknown) => Promise<unknown>> })
+      .handlers.get('extract');
+    await extractHandler!({
+      data: extractJobs[0].data,
+      signal: { aborted: false },
+      updateProgress: async () => {},
+    });
+    const links = await engine.getLinks('notes/n0');
+    expect(links.some(l => l.to_slug === 'people/alice')).toBe(true);
+    const rows = await engine.executeRaw<{ links_extracted_at: string | null }>(
+      `SELECT links_extracted_at FROM pages WHERE slug = 'notes/n0'`,
+    );
+    expect(rows[0]?.links_extracted_at).not.toBeNull();
+  }, 180_000);
+
+  test('sub-threshold sync does NOT set extractDeferred (no spurious follow-up)', async () => {
+    // One more small commit → inline extract path, no deferral.
+    writeFileSync(join(repoPath, 'notes/small.md'), [
+      '---', 'type: note', 'title: Small', '---', '', 'No big deal.',
+    ].join('\n'));
+    git('git add -A && git commit -m "one small page"');
+    const { performSync } = await import('../src/commands/sync.ts');
+    const result = await performSync(engine, { repoPath, noPull: true, noEmbed: true });
+    expect(result.status).toBe('synced');
+    expect(result.extractDeferred).toBeFalsy();
+  }, 60_000);
+});

test/sync-trigger-cli.test.ts

@@ -100,6 +100,10 @@ describe('runSyncTrigger', () => {
     const job = jobs[0];
     expect(job.priority).toBe(-10);
     expect((job.data as { sourceId: string }).sourceId).toBe('default');
+    // #2849: opt in to inline extraction — the standalone sync handler
+    // defaults noExtract to TRUE, which would leave triggered syncs
+    // extraction-stale.
+    expect((job.data as { noExtract: boolean }).noExtract).toBe(false);
     expect((job.data as { auto_embed_backfill: boolean }).auto_embed_backfill).toBe(true);
   });