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/config.ts

@@ -908,10 +908,6 @@ export const KNOWN_CONFIG_KEYS: readonly string[] = [
   'facts.extraction_model',
   // #2113: output-token cap for the per-turn facts extractor (default 4000).
   'facts.extraction_max_tokens',
-  // Owner opt-in: let the local stdio MCP pipe read this owner's private facts
-  // (find_trajectory / recall). Default off; HTTP transport ignores it. See
-  // src/core/facts/reader-trust.ts.
-  'facts.trust_local_reads',
   // Dream cycle config
   'dream.synthesize.session_corpus_dir',
   'dream.synthesize.meeting_transcripts_dir',

src/core/engine.ts

@@ -591,8 +591,6 @@ export interface TrajectoryOpts {
   sourceIds?: string[];
   /** When true, filters to visibility='world' only. Set by MCP layer from ctx.remote. */
   remote?: boolean;
-  /** Owner opt-in: read private facts despite `remote`. See facts/reader-trust.ts. */
-  trustedFactReads?: boolean;
   /** Metric filter. When set, only facts with this canonical metric label participate. */
   metric?: string;
   /**

src/core/facts/meta-hook.ts

@@ -17,7 +17,6 @@
 import type { OperationContext } from './../operations.ts';
 import type { FactRow } from './../engine.ts';
 import { effectiveConfidence } from './decay.ts';
-import { readableFactVisibilities } from './reader-trust.ts';
 
 const DEFAULT_TTL_MS = 30_000;
 const DEFAULT_TOP_K = 10;
@@ -51,13 +50,7 @@ export async function getBrainHotMemoryMeta(
   const sessionId = (ctx as { source_session?: string }).source_session
     ?? null;
   const allowListHash = hashAllowList(ctx.takesHoldersAllowList);
-  // Visibility tier: untrusted remote → world-only; trusted local +
-  // owner-trusted reads → all rows. Folded into the cache key (the header's
-  // "cache entries don't bleed across tiers" invariant): trustedFactReads is
-  // re-read from config per call, so a mid-session opt-out must not keep
-  // serving a private-inclusive cached payload for the TTL window.
-  const visibility = readableFactVisibilities(ctx);
-  const cacheKey = `${sourceId}::${sessionId ?? '_'}::${allowListHash}::${visibility ? 'world' : 'all'}`;
+  const cacheKey = `${sourceId}::${sessionId ?? '_'}::${allowListHash}`;
 
   const ttl = Math.max(1000, opts.ttlMs ?? DEFAULT_TTL_MS);
   const topK = Math.max(1, Math.min(opts.topK ?? DEFAULT_TOP_K, 25));
@@ -68,6 +61,10 @@ export async function getBrainHotMemoryMeta(
     return cached.payload;
   }
 
+  // Build a fresh payload. Visibility tier: remote → world-only;
+  // local → all rows.
+  const visibility = ctx.remote === false ? undefined : ['world'] as ('world' | 'private')[];
+
   let rows: FactRow[] = [];
   if (sessionId) {
     rows = await ctx.engine.listFactsBySession(sourceId, sessionId, {

src/core/facts/reader-trust.ts

@@ -1,48 +0,0 @@
-/**
- * Fact-read visibility trust.
- *
- * Fact rows are tagged `private` | `world`. Remote/untrusted callers
- * (`remote === true`) see only `world` rows — the posture that keeps a
- * published or HTTP-served brain from leaking private claims to strangers.
- *
- * But the stdio MCP server is an unauthenticated LOCAL pipe: on a single-owner
- * machine the caller IS the owner, yet it still defaults `remote: true` for
- * safety, so the owner's own agent is denied the owner's own private facts
- * (e.g. `find_trajectory` returns empty over MCP even though the facts exist).
- *
- * `trustedFactReads` is a narrow, READ-ONLY trust elevation, deliberately
- * DECOUPLED from `remote` so every other remote protection — file_upload
- * confinement, source isolation, fence stripping, takes-holder scoping — stays
- * fully in force. The stdio MCP server sets it ONLY when the brain owner opts
- * in via the `facts.trust_local_reads` config (default off). The HTTP/published
- * transport never sets it, so a served brain stays world-only regardless.
- */
-export interface FactReaderTrust {
-  /**
-   * Mirrors OperationContext.remote. FAIL-CLOSED: anything not strictly
-   * `false` is treated as remote/untrusted (CLAUDE.md trust invariant).
-   */
-  remote?: boolean;
-  /** Owner opt-in: this remote caller may read private facts. */
-  trustedFactReads?: boolean;
-}
-
-/**
- * True when the reader is restricted to `visibility = 'world'` rows.
- * Fail-closed: an unset/undefined `remote` is untrusted — only an explicit
- * `remote: false` (trusted local CLI) or an explicit owner opt-in
- * (`trustedFactReads: true`) reads private rows.
- */
-export function factsWorldOnly(t: FactReaderTrust): boolean {
-  return t.remote !== false && t.trustedFactReads !== true;
-}
-
-/**
- * Visibility filter for list-style fact reads: `['world']` when the reader is
- * world-only, `undefined` (no filter — all rows) when it is trusted.
- */
-export function readableFactVisibilities(
-  t: FactReaderTrust,
-): ('private' | 'world')[] | undefined {
-  return factsWorldOnly(t) ? ['world'] : undefined;
-}

src/core/operations.ts

@@ -18,7 +18,6 @@ import { captureEvalCandidate, isEvalCaptureEnabled, isEvalScrubEnabled } from '
 import type { HybridSearchMeta } from './types.ts';
 import { extractPageLinks, isAutoLinkEnabled, isAutoTimelineEnabled, isGlobalBasenameEnabled, parseTimelineEntries, makeResolver, type UnresolvedFrontmatterRef } from './link-extraction.ts';
 import { isFactsBackstopEligible } from './facts/eligibility.ts';
-import { readableFactVisibilities } from './facts/reader-trust.ts';
 import { stripTakesFence } from './takes-fence.ts';
 import { stripFactsFence } from './facts-fence.ts';
 import { getContentFlag } from './quarantine.ts';
@@ -333,15 +332,6 @@ export interface OperationContext {
    * remote/untrusted (defense in depth in case the type is bypassed via cast).
    */
   remote: boolean;
-  /**
-   * Owner opt-in (`facts.trust_local_reads`): allow this remote caller to read
-   * `private` facts. A NARROW, read-only trust elevation decoupled from
-   * `remote` — every other remote protection (file confinement, source
-   * isolation, fence stripping, takes scoping) stays in force. Set ONLY by the
-   * stdio MCP server when the config is on; the HTTP transport never sets it.
-   * Consulted via `src/core/facts/reader-trust.ts`.
-   */
-  trustedFactReads?: boolean;
   /**
    * Subagent runtime context (v0.16+). Set by the subagent tool dispatcher when
    * dispatching an op as a tool call from an LLM loop. Used to enforce per-op
@@ -3639,7 +3629,6 @@ const find_trajectory: Operation = {
       entitySlug: p.entity_slug,
       ...scope,
       remote: ctx.remote === true,
-      trustedFactReads: ctx.trustedFactReads === true,
       metric,
       kind,
       since,
@@ -4000,9 +3989,13 @@ const recall: Operation = {
     const includeExpired = p.include_expired === true;
     const grep = typeof p.grep === 'string' ? p.grep.toLowerCase() : null;
 
-    // Visibility filter: world-only for untrusted remote callers; all rows for
-    // trusted local CLI and owner-trusted reads (facts.trust_local_reads).
-    const visibility = readableFactVisibilities(ctx);
+    // Visibility filter: remote callers see world-only unless their token
+    // grants elevated visibility (future-proofing; v0.31 ships world-only
+    // for remote, all for local CLI).
+    const visibility =
+      ctx.remote === false
+        ? undefined
+        : ['world'] as ('private' | 'world')[];
 
     let rows: Awaited<ReturnType<typeof ctx.engine.listFactsByEntity>> = [];
 

src/core/pglite-engine.ts

@@ -18,7 +18,6 @@ import type {
 } from './engine.ts';
 import { MAX_SEARCH_LIMIT, clampSearchLimit } from './engine.ts';
 import { withRetry, BULK_RETRY_OPTS, resolveBulkRetryOpts, computeNextDelay, type BatchAuditSite } from './retry.ts';
-import { factsWorldOnly } from './facts/reader-trust.ts';
 import { logBatchRetry as auditLogBatchRetry, logBatchExhausted as auditLogBatchExhausted } from './audit/batch-retry-audit.ts';
 import { runMigrations } from './migrate.ts';
 import { PGLITE_SCHEMA_SQL, getPGLiteSchema } from './pglite-schema.ts';
@@ -4319,10 +4318,7 @@ export class PGLiteEngine implements BrainEngine {
     const useArray = Array.isArray(opts.sourceIds) && opts.sourceIds.length > 0;
     const sourceIds = useArray ? opts.sourceIds! : null;
     const sourceId = opts.sourceId ?? 'default';
-    // Direct-engine contract: unset `remote` here means a trusted in-process
-    // caller (CLI/tests) — the fail-closed default lives in the op layer, which
-    // always passes explicit booleans. Normalize before the fail-closed helper.
-    const remoteFilter = factsWorldOnly({ remote: opts.remote === true, trustedFactReads: opts.trustedFactReads === true });
+    const remoteFilter = opts.remote === true;
 
     // Build SQL dynamically. PGLite uses $N positional params; we
     // assemble the WHERE clauses + params array in tandem to keep them

src/core/postgres-engine.ts

@@ -14,7 +14,6 @@ import type {
   SourceRow,
 } from './engine.ts';
 import { withRetry, BULK_RETRY_OPTS, resolveBulkRetryOpts, computeNextDelay, type BatchAuditSite } from './retry.ts';
-import { factsWorldOnly } from './facts/reader-trust.ts';
 import { logBatchRetry as auditLogBatchRetry, logBatchExhausted as auditLogBatchExhausted } from './audit/batch-retry-audit.ts';
 import type {
   DomainBankSampleOpts, CorpusSampleOpts, DomainBankRow,
@@ -4533,10 +4532,7 @@ export class PostgresEngine implements BrainEngine {
     const useArray = Array.isArray(opts.sourceIds) && opts.sourceIds.length > 0;
     const sourceIds = useArray ? opts.sourceIds! : null;
     const sourceId = opts.sourceId ?? 'default';
-    // Direct-engine contract: unset `remote` here means a trusted in-process
-    // caller (CLI/tests) — the fail-closed default lives in the op layer, which
-    // always passes explicit booleans. Normalize before the fail-closed helper.
-    const remoteFilter = factsWorldOnly({ remote: opts.remote === true, trustedFactReads: opts.trustedFactReads === true });
+    const remoteFilter = opts.remote === true;
 
     // Source-scope predicate: array path (federated) wins over scalar.
     // Engine.ts contract: returns chronological points; regressions +

src/mcp/dispatch.ts

@@ -30,13 +30,6 @@ export interface ToolResult {
 export interface DispatchOpts {
   /** Defaults to true (remote/untrusted). Local CLI callers (`gbrain call`) pass false. */
   remote?: boolean;
-  /**
-   * Owner opt-in (`facts.trust_local_reads`): let this remote caller read
-   * `private` facts. Set ONLY by the stdio MCP server; the HTTP transport
-   * leaves it unset so a served brain stays world-only. See
-   * `src/core/facts/reader-trust.ts`.
-   */
-  trustedFactReads?: boolean;
   /** Override the default stderr logger (e.g. CLI uses console.* directly). */
   logger?: OperationContext['logger'];
   /**
@@ -210,7 +203,6 @@ export function buildOperationContext(
     logger: opts.logger || stderrLogger,
     dryRun: !!params.dry_run,
     remote: opts.remote ?? true,
-    trustedFactReads: opts.trustedFactReads === true,
     takesHoldersAllowList: opts.takesHoldersAllowList,
     // v0.34 D4: sourceId is REQUIRED at the type level. Auto-fill 'default'
     // for single-source brains and any caller who didn't resolve a sourceId.

src/mcp/server.ts

@@ -35,16 +35,6 @@ export async function startMcpServer(engine: BrainEngine) {
   // shape and cast through `any` (the SDK accepts it via the ServerResult union).
   server.setRequestHandler(CallToolRequestSchema, async (request: any): Promise<any> => {
     const { name, arguments: params } = request.params;
-    // Owner opt-in: the stdio pipe is local + unauthenticated, so on a
-    // single-owner machine its caller is the owner. When facts.trust_local_reads
-    // is on, let fact reads (find_trajectory / recall) see this owner's own
-    // private facts. Narrow + read-only — every other remote protection stays
-    // on (remote stays true). HTTP transport never sets this. Best-effort: a
-    // config read blip falls back to the safe world-only default.
-    let trustedFactReads = false;
-    try {
-      trustedFactReads = (await engine.getConfig('facts.trust_local_reads')) === 'true';
-    } catch { /* keep world-only default */ }
     // v0.28: stdio MCP has no per-token auth (local pipe). Default the
     // takes-holder allow-list to ['world'] so agent-facing callers don't
     // see private hunches via takes_list / takes_search / query. Operators
@@ -52,7 +42,6 @@ export async function startMcpServer(engine: BrainEngine) {
     // `gbrain call <op>` (sets remote=false in src/cli.ts).
     return dispatchToolCall(engine, name, params, {
       remote: true,
-      trustedFactReads,
       takesHoldersAllowList: ['world'],
       // v0.31: source defaults to 'default' for stdio (no per-token scope).
       // Operators who want a different source on stdio MCP should set

test/engine-find-trajectory.test.ts

@@ -165,22 +165,6 @@ describe('findTrajectory — visibility filter (D-CDX-1 / R6)', () => {
     const all = await engine.findTrajectory({ entitySlug: 'traj-vis-default' });
     expect(all.length).toBe(2);
   });
-
-  test('remote=true + trustedFactReads bypasses world-only (owner-trusted reads)', async () => {
-    await insertTyped({ entity_slug: 'traj-vis-trusted', metric: 'mrr', value: 50000, visibility: 'private', valid_from: new Date('2026-01-15') });
-    await insertTyped({ entity_slug: 'traj-vis-trusted', metric: 'mrr', value: 99999, visibility: 'world',   valid_from: new Date('2026-04-12') });
-
-    // Untrusted remote: world only.
-    const untrusted = await engine.findTrajectory({ entitySlug: 'traj-vis-trusted', remote: true });
-    expect(untrusted.length).toBe(1);
-    expect(untrusted[0].value).toBe(99999);
-
-    // Owner-trusted remote: sees the private point too. remote stays true — only
-    // fact-read visibility is elevated.
-    const trusted = await engine.findTrajectory({ entitySlug: 'traj-vis-trusted', remote: true, trustedFactReads: true });
-    expect(trusted.length).toBe(2);
-    expect(trusted.map(p => p.value).sort((a, b) => (a! - b!))).toEqual([50000, 99999]);
-  });
 });
 
 describe('findTrajectory — metric + since + until filters', () => {

test/facts-reader-trust.test.ts

@@ -1,43 +0,0 @@
-import { describe, test, expect } from 'bun:test';
-import {
-  factsWorldOnly,
-  readableFactVisibilities,
-} from '../src/core/facts/reader-trust.ts';
-
-describe('factsWorldOnly', () => {
-  test('FAIL-CLOSED: unset remote is untrusted (world-only)', () => {
-    expect(factsWorldOnly({})).toBe(true);
-    expect(factsWorldOnly({ remote: undefined })).toBe(true);
-    expect(factsWorldOnly({ trustedFactReads: false })).toBe(true);
-  });
-
-  test('explicit remote=false (trusted local CLI) sees all', () => {
-    expect(factsWorldOnly({ remote: false })).toBe(false);
-    expect(factsWorldOnly({ remote: false, trustedFactReads: false })).toBe(false);
-  });
-
-  test('untrusted remote callers are world-only', () => {
-    expect(factsWorldOnly({ remote: true })).toBe(true);
-    expect(factsWorldOnly({ remote: true, trustedFactReads: false })).toBe(true);
-  });
-
-  test('owner-trusted remote reads bypass the world-only filter', () => {
-    expect(factsWorldOnly({ remote: true, trustedFactReads: true })).toBe(false);
-  });
-
-  test('trustedFactReads is a no-op for an already-trusted local caller', () => {
-    expect(factsWorldOnly({ remote: false, trustedFactReads: true })).toBe(false);
-  });
-});
-
-describe('readableFactVisibilities', () => {
-  test("world-only readers get the ['world'] filter (incl. unset remote)", () => {
-    expect(readableFactVisibilities({ remote: true })).toEqual(['world']);
-    expect(readableFactVisibilities({})).toEqual(['world']);
-  });
-
-  test('trusted readers get undefined (no filter — all rows)', () => {
-    expect(readableFactVisibilities({ remote: false })).toBeUndefined();
-    expect(readableFactVisibilities({ remote: true, trustedFactReads: true })).toBeUndefined();
-  });
-});

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);
   });