fix: community fix wave — 10 PRs, 7 contributors (v0.9.1) (#65)

* fix: security hardening — search DoS, slug hijack, symlink traversal, content bombs, stdin guard

4 security vulnerabilities closed:
- Search limit clamped to 100 (MAX_SEARCH_LIMIT) with statement_timeout 8s
- Frontmatter slug authority enforced (path-derived, mismatch rejected)
- Symlink traversal blocked (lstatSync in walker + importFromFile)
- Content size guard on importFromContent (Buffer.byteLength, 5MB)
- Stdin size guard in parseOpArgs (5MB cap)

Search pagination added (--offset param on search + query operations).
Clamp warning emitted when limit is capped.

Co-Authored-By: garagon <garagon@users.noreply.github.com>

* fix: PGLite concurrent access lock — prevent Aborted() crash

File-based advisory lock using atomic mkdir with PID tracking
and 5-minute stale detection. Clear error messages show which
process holds the lock and how to recover.

Co-Authored-By: danbr <danbr@users.noreply.github.com>

* fix: 12 data integrity fixes + stale embedding prevention

CTE searchKeyword rewrite (SQL-level LIMIT, not JS splice).
Write validation on addLink/addTag/addTimelineEntry/putRawData/createVersion.
Health metrics now measure real problems (stale_pages, orphan_pages, dead_links).
Orphan chunk cleanup on empty pages. Embedding error logging.
contentHash now covers all PageInput fields.
Stale embedding NULL'd when chunk_text changes (prevents wrong vector on new text).
hybridSearch stops double-embedding query. MCP param validation.
type/exclude_slugs search filters now work. pgcrypto extension for Postgres <13.

Co-Authored-By: win4r <win4r@users.noreply.github.com>

* perf: 30x embedAll speedup + O(n²) fix + ask alias

Sliding worker pool (concurrency 20, tunable via GBRAIN_EMBED_CONCURRENCY).
O(n²) chunk lookup in embedPage replaced with Map.
gbrain ask alias for query (CLI-only, not in MCP tools-json).
.idea added to .gitignore.

Co-Authored-By: stephenhungg <stephenhungg@users.noreply.github.com>
Co-Authored-By: sharziki <sharziki@users.noreply.github.com>
Co-Authored-By: hnshah <hnshah@users.noreply.github.com>
Co-Authored-By: doguabaris <doguabaris@users.noreply.github.com>

* chore: bump version and changelog (v0.9.1)

Community fix wave: 10 PRs, 7 contributors.
4 security fixes, PGLite crash fix, 12 data integrity fixes,
30x embed speedup, search pagination, ask alias.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: garagon <garagon@users.noreply.github.com>
Co-authored-by: danbr <danbr@users.noreply.github.com>
Co-authored-by: win4r <win4r@users.noreply.github.com>
Co-authored-by: stephenhungg <stephenhungg@users.noreply.github.com>
Co-authored-by: sharziki <sharziki@users.noreply.github.com>
Co-authored-by: hnshah <hnshah@users.noreply.github.com>
Co-authored-by: doguabaris <doguabaris@users.noreply.github.com>
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

test/cli.test.ts

@@ -40,6 +40,26 @@ describe('CLI version', () => {
   });
 });
 
+describe('ask alias', () => {
+  test('ask alias maps to query in source', () => {
+    expect(cliSource).toContain("if (command === 'ask')");
+    expect(cliSource).toContain("command = 'query'");
+  });
+
+  test('ask does NOT appear in --tools-json output', async () => {
+    const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', '--tools-json'], {
+      cwd: new URL('..', import.meta.url).pathname,
+      stdout: 'pipe',
+      stderr: 'pipe',
+    });
+    const stdout = await new Response(proc.stdout).text();
+    await proc.exited;
+    const tools = JSON.parse(stdout);
+    const names = tools.map((t: any) => t.name);
+    expect(names).not.toContain('ask');
+  });
+});
+
 describe('CLI dispatch integration', () => {
   test('--version outputs version', async () => {
     const proc = Bun.spawn(['bun', 'run', 'src/cli.ts', '--version'], {