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>

docs/tutorials/company-brain.md

@@ -223,16 +223,14 @@ export GBRAIN_REMOTE_CLIENT_ID=<Alice's client_id>
 export GBRAIN_REMOTE_CLIENT_SECRET=<Alice's client_secret>
 export GBRAIN_REMOTE_MCP_URL=https://brain.acme-co.com/mcp
 
-gbrain search "performance review"
+gbrain search "performance review" --remote
 ```
 
-(On a thin-client install every shared op routes through the remote MCP server automatically — no flag needed. The env vars select whose credentials the call uses.)
-
 Alice should see results only from `customers` and `shared`. The performance-review notes live in `internal`, which she's not scoped to read. She shouldn't see them.
 
 ```bash
 # Terminal 2, as Bob (export his credentials similarly)
-gbrain search "performance review"
+gbrain search "performance review" --remote
 ```
 
 Bob should see the performance-review notes from `internal`, plus anything related from `shared`. He shouldn't see anything that lives only in `customers`.
@@ -516,7 +514,7 @@ The first sync embeds every page, which takes time. Check `gbrain sources status
 
 ### "I see a page I shouldn't see"
 
-This shouldn't happen, but if you suspect it, run `gbrain search <query> --json` as the constrained client (thin-client install, with the client's `GBRAIN_REMOTE_*` env exported) and inspect the `source_id` field on every returned result. Every row should be in the client's `--federated-read` set. If one isn't, file an issue with the exact slug and source IDs.
+This shouldn't happen, but if you suspect it, run `gbrain search <query> --remote --json` as the constrained client and inspect the `source_id` field on every returned result. Every row should be in the client's `--federated-read` set. If one isn't, file an issue with the exact slug and source IDs.
 
 ### "The synthesized answer is wrong"
 

src/cli.ts

@@ -464,11 +464,7 @@ async function main() {
     // routed path. Date → ISO string; bigint → string (postgres.js shape);
     // Buffer → object. Microsecond-cost; eliminates a whole drift bug class.
     const result = JSON.parse(JSON.stringify(rawResult, bigintToStringReplacer));
-    // #380 pass-through: `--json` (undeclared on most ops, promised by docs)
-    // emits the raw op result instead of the human formatter.
-    const output = params.json === true
-      ? JSON.stringify(result, null, 2) + '\n'
-      : formatResult(op.name, result);
+    const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     // v0.42.20.0 (codex D4): on error, set exitCode + return so the `finally`
@@ -551,10 +547,7 @@ async function runThinClientRouted(
       signal: sigintController.signal,
     });
     const result = unpackToolResult(raw);
-    // #380: same --json seam as the local-engine path (renderer parity).
-    const output = params.json === true
-      ? JSON.stringify(result, null, 2) + '\n'
-      : formatResult(op.name, result);
+    const output = formatResult(op.name, result);
     if (output) process.stdout.write(output);
   } catch (e: unknown) {
     if (e instanceof RemoteMcpError) {
@@ -764,28 +757,10 @@ export function resolveQueryImage(
   return { path: imagePath, base64, mime };
 }
 
-/**
- * #380: undeclared flags that are honored DOWNSTREAM of parseOpArgs and must
- * keep passing through when unknown flags become hard errors:
- *   - source     → makeContext's resolveSourceId (the --source axis)
- *   - brain      → the mount/brain routing axis (docs promise the flag)
- *   - dry_run    → makeContext's ctx.dryRun (ops without a declared dry_run)
- *   - json       → raw-JSON output seam (local + thin-client paths)
- */
-const PASSTHROUGH_VALUE_FLAGS = new Set(['source', 'brain']);
-const PASSTHROUGH_BOOL_FLAGS = new Set(['dry_run', 'json']);
-
 export function parseOpArgs(op: Operation, args: string[]): Record<string, unknown> {
   const params: Record<string, unknown> = {};
   const positional = op.cliHints?.positional || [];
   let posIdx = 0;
-  const cliName = op.cliHints?.name || op.name;
-  const MAX_STDIN = 5_000_000; // 5MB cap, shared by stdin and --file
-  // #380: `--file <path>` fills the op's declared stdin param (put's `content`)
-  // from a file. Driven by cliHints.stdin — no per-op hard-coding — and
-  // disabled when the op declares a real `file` param of its own.
-  const fileParam = op.cliHints?.stdin && !op.params.file ? op.cliHints.stdin : undefined;
-  let filePath: string | undefined;
 
   for (let i = 0; i < args.length; i++) {
     const arg = args[i];
@@ -799,42 +774,12 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
         }
       }
       const key = arg.slice(2).replace(/-/g, '_');
-      if (fileParam && key === 'file') {
-        if (i + 1 >= args.length) {
-          console.error(`Error: ${arg} requires a value.`);
-          process.exit(1);
-        }
-        filePath = args[++i];
-        continue;
-      }
       const paramDef = op.params[key];
-      if (!paramDef) {
-        if (PASSTHROUGH_BOOL_FLAGS.has(key)) {
-          params[key] = true;
-          continue;
-        }
-        if (PASSTHROUGH_VALUE_FLAGS.has(key)) {
-          if (i + 1 >= args.length) {
-            console.error(`Error: ${arg} requires a value.`);
-            process.exit(1);
-          }
-          params[key] = args[++i];
-          continue;
-        }
-        // #380: unknown flags were silently swallowed into params, so typos
-        // like `put --file` created empty pages instead of erroring.
-        console.error(`Unknown option for gbrain ${cliName}: ${arg}`);
-        console.error(`Run 'gbrain ${cliName} --help' for valid flags.`);
-        process.exit(1);
-      }
-      if (paramDef.type === 'boolean') {
+      if (paramDef?.type === 'boolean') {
         params[key] = true;
       } else if (i + 1 < args.length) {
         params[key] = args[++i];
-        if (paramDef.type === 'number') params[key] = Number(params[key]);
-      } else {
-        console.error(`Error: ${arg} requires a value.`);
-        process.exit(1);
+        if (paramDef?.type === 'number') params[key] = Number(params[key]);
       }
     } else if (posIdx < positional.length) {
       const key = positional[posIdx++];
@@ -843,30 +788,10 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
     }
   }
 
-  // #380: resolve --file AFTER the loop so --file/--content conflicts are
-  // caught in either order.
-  if (filePath !== undefined && fileParam) {
-    if (params[fileParam] !== undefined) {
-      console.error(`Error: use only one of --file, --${fileParam}, or stdin for gbrain ${cliName}.`);
-      process.exit(1);
-    }
-    let fileContent: string;
-    try {
-      fileContent = readFileSync(filePath, 'utf-8');
-    } catch (e) {
-      console.error(`Error: cannot read --file ${filePath}: ${e instanceof Error ? e.message : String(e)}`);
-      process.exit(1);
-    }
-    if (Buffer.byteLength(fileContent, 'utf-8') > MAX_STDIN) {
-      console.error(`Error: file content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
-      process.exit(1);
-    }
-    params[fileParam] = fileContent;
-  }
-
   // Read stdin for content params
   if (op.cliHints?.stdin && !params[op.cliHints.stdin] && !process.stdin.isTTY) {
     const stdinContent = readFileSync(0, 'utf-8');
+    const MAX_STDIN = 5_000_000; // 5MB
     if (Buffer.byteLength(stdinContent, 'utf-8') > MAX_STDIN) {
       console.error(`Error: stdin content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
@@ -2328,10 +2253,6 @@ export function printOpHelp(op: Operation, invokedName?: string) {
       const prefix = isPos ? `  <${key}>` : `  --${key.replace(/_/g, '-')}`;
       console.log(`${prefix.padEnd(28)} ${def.description || ''}${req}`);
     }
-    // #380: ops that read stdin also accept --file <path> (parseOpArgs).
-    if (op.cliHints?.stdin && !op.params.file) {
-      console.log(`${'  --file <path>'.padEnd(28)} Read ${op.cliHints.stdin} from a file (alternative to --${op.cliHints.stdin} or stdin)`);
-    }
   }
 }
 

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/operations.ts

@@ -769,7 +769,7 @@ const get_page: Operation = {
 
 const put_page: Operation = {
   name: 'put_page',
-  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. On the CLI, `gbrain put SLUG --file PATH` reads content from a file (also `--content` or stdin). For provenance write-through and a binary-NUL guard, prefer `gbrain capture --file PATH --slug SLUG` (v0.39.3.0).',
+  description: 'Write/update a page (markdown with frontmatter). Chunks, embeds, reconciles tags, and (when auto_link/auto_timeline are enabled) extracts + reconciles graph links and timeline entries. For large content on Windows (pipe-buffer limit ~45KB) or any file-as-input workflow, use `gbrain capture --file PATH --slug SLUG` — capture reads the file as a Buffer with a binary-NUL guard and adds provenance write-through (v0.39.3.0).',
   params: {
     slug: { type: 'string', required: true, description: 'Page slug' },
     content: { type: 'string', required: true, description: 'Full markdown content with YAML frontmatter' },
@@ -1384,10 +1384,7 @@ const list_pages: Operation = {
   params: {
     type: { type: 'string', description: 'Filter by page type' },
     tag: { type: 'string', description: 'Filter by tag' },
-    limit: { type: 'number', description: 'Max results (default 50, capped at 100 — use offset to paginate beyond)' },
-    // #2876: the 100-row cap was silent and there was no way past it even
-    // though both engines already support OFFSET on listPages.
-    offset: { type: 'number', description: 'Skip first N results (pagination; pair with limit)' },
+    limit: { type: 'number', description: 'Max results (default 50)' },
     // v0.29 — surface filter that already exists on PageFilters.
     updated_after: {
       type: 'string',
@@ -1418,10 +1415,6 @@ const list_pages: Operation = {
       type: p.type as any,
       tag: p.tag as string,
       limit: clampSearchLimit(p.limit as number | undefined, 50, 100),
-      // #2876: thread pagination through (engines already honor offset).
-      offset: Number.isFinite(p.offset as number) && (p.offset as number) > 0
-        ? Math.floor(p.offset as number)
-        : undefined,
       includeDeleted: (p.include_deleted as boolean) === true,
       updated_after: typeof p.updated_after === 'string' ? p.updated_after : undefined,
       sort,

test/cli-args.test.ts

@@ -1,41 +1,8 @@
 import { describe, expect, test } from 'bun:test';
-import { mkdtempSync, rmSync, writeFileSync } from 'fs';
-import { tmpdir } from 'os';
-import { join } from 'path';
 import { parseOpArgs } from '../src/cli.ts';
 import { operationsByName } from '../src/core/operations.ts';
 
 describe('parseOpArgs', () => {
-  // #380: `gbrain put SLUG --file PATH` reads content from the file instead
-  // of silently swallowing the flag and creating an empty page.
-  test('put --file reads the stdin param (content) from a file', () => {
-    const dir = mkdtempSync(join(tmpdir(), 'gbrain-put-file-'));
-    try {
-      const pagePath = join(dir, 'page.md');
-      writeFileSync(pagePath, '# From file\n\nBody loaded from --file.\n');
-      const params = parseOpArgs(operationsByName.put_page, ['concepts/from-file', '--file', pagePath]);
-      expect(params.slug).toBe('concepts/from-file');
-      expect(params.content).toBe('# From file\n\nBody loaded from --file.\n');
-    } finally {
-      rmSync(dir, { recursive: true, force: true });
-    }
-  });
-
-  // #380 regression guard: undeclared-but-honored flags must keep passing
-  // through when unknown flags become hard errors (--source is read by
-  // makeContext; --json by the output seam; --dry-run by ctx.dryRun).
-  test('pass-through allowlist flags survive on ops that do not declare them', () => {
-    const params = parseOpArgs(operationsByName.get_page, [
-      'people/alice-example', '--source', 'wiki', '--json', '--dry-run',
-    ]);
-    expect(params).toEqual({
-      slug: 'people/alice-example',
-      source: 'wiki',
-      json: true,
-      dry_run: true,
-    });
-  });
-
   test('--no-<boolean> maps to false without consuming the next flag', () => {
     const params = parseOpArgs(operationsByName.query, [
       'freshEmbedSourceScope code source',

test/cli.test.ts

@@ -1,5 +1,5 @@
 import { describe, test, expect } from 'bun:test';
-import { existsSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from 'fs';
+import { existsSync, mkdtempSync, readFileSync, rmSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
 
@@ -120,76 +120,6 @@ describe('CLI dispatch integration', () => {
     expect(exitCode).toBe(0);
   });
 
-  // #380 / PR #856: put --help documents the --file input path.
-  test('put --help documents --file input', async () => {
-    const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'put', '--help'], {
-      cwd: repoRoot,
-      stdout: 'pipe',
-      stderr: 'pipe',
-    });
-    const stdout = await new Response(proc.stdout).text();
-    const exitCode = await proc.exited;
-    expect(stdout).toContain('Usage: gbrain put');
-    expect(stdout).toContain('--file <path>');
-    expect(exitCode).toBe(0);
-  });
-
-  // #380: unknown flags on shared ops are a hard error (previously silently
-  // swallowed into params — `put --file` created empty pages). parseOpArgs
-  // runs BEFORE engine connect, so the error must fire without a brain.
-  test('unknown shared-op flags fail before DB connection', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-unknown-flag-'));
-    try {
-      const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'get', 'people/alice', '--bogus'], {
-        cwd: repoRoot,
-        stdout: 'pipe',
-        stderr: 'pipe',
-        env: isolatedEnv(home),
-      });
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('Unknown option for gbrain get: --bogus');
-      expect(stderr).not.toContain('No brain configured');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
-  test('put rejects combining --file and --content', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-put-conflict-'));
-    try {
-      const pagePath = join(home, 'page.md');
-      writeFileSync(pagePath, 'file body\n');
-      const proc = Bun.spawn(
-        ['bun', 'run', 'src/cli.ts', 'put', 'a/b', '--content', 'inline', '--file', pagePath],
-        { cwd: repoRoot, stdout: 'pipe', stderr: 'pipe', env: isolatedEnv(home) },
-      );
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('use only one of --file, --content, or stdin');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
-  test('put --file with a missing path errors instead of writing an empty page', async () => {
-    const home = mkdtempSync(join(tmpdir(), 'gbrain-cli-put-missing-file-'));
-    try {
-      const proc = Bun.spawn(
-        ['bun', 'run', 'src/cli.ts', 'put', 'a/b', '--file', join(home, 'nope.md')],
-        { cwd: repoRoot, stdout: 'pipe', stderr: 'pipe', env: isolatedEnv(home) },
-      );
-      const stderr = await new Response(proc.stderr).text();
-      const exitCode = await proc.exited;
-      expect(stderr).toContain('cannot read --file');
-      expect(exitCode).toBe(1);
-    } finally {
-      rmSync(home, { recursive: true, force: true });
-    }
-  });
-
   test('upgrade --help prints usage without running upgrade', async () => {
     const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', 'upgrade', '--help'], {
       cwd: repoRoot,

test/list-pages-offset.test.ts

@@ -1,55 +0,0 @@
-import { describe, test, expect } from 'bun:test';
-import { operationsByName } from '../src/core/operations.ts';
-
-/**
- * #2876: `gbrain list --limit` silently clamped at 100 with no pagination.
- * list_pages now declares `offset` (both engines already supported it on
- * PageFilters) and the limit description discloses the 100-row cap.
- */
-describe('list_pages pagination (#2876)', () => {
-  const listPagesOp = operationsByName.list_pages;
-
-  function makeCtx(captured: unknown[]) {
-    return {
-      engine: {
-        listPages: async (filters: unknown) => {
-          captured.push(filters);
-          return [];
-        },
-      },
-      config: { engine: 'pglite' },
-      logger: { info() {}, warn() {}, error() {} },
-      dryRun: false,
-      remote: false,
-      sourceId: 'default',
-    } as any;
-  }
-
-  test('declares offset param and discloses the 100-row cap on limit', () => {
-    expect(listPagesOp.params.offset).toBeDefined();
-    expect(listPagesOp.params.offset.type).toBe('number');
-    expect(listPagesOp.params.limit.description).toContain('100');
-  });
-
-  test('threads offset through to engine.listPages', async () => {
-    const captured: any[] = [];
-    await listPagesOp.handler(makeCtx(captured), { limit: 10, offset: 30 });
-    expect(captured[0].offset).toBe(30);
-    expect(captured[0].limit).toBe(10);
-  });
-
-  test('drops negative, non-finite, and zero offsets', async () => {
-    const captured: any[] = [];
-    const ctx = makeCtx(captured);
-    await listPagesOp.handler(ctx, { offset: -5 });
-    await listPagesOp.handler(ctx, { offset: Infinity });
-    await listPagesOp.handler(ctx, { offset: 0 });
-    for (const f of captured) expect(f.offset).toBeUndefined();
-  });
-
-  test('floors fractional offsets', async () => {
-    const captured: any[] = [];
-    await listPagesOp.handler(makeCtx(captured), { offset: 7.9 });
-    expect(captured[0].offset).toBe(7);
-  });
-});

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);
   });