fix(extract): default --dir to configured brain dir, not cwd

src/commands/extract.ts

@@ -354,7 +354,19 @@ export async function runExtractCore(engine: BrainEngine, opts: ExtractOpts): Pr
 export async function runExtract(engine: BrainEngine, args: string[]) {
   const subcommand = args[0];
   const dirIdx = args.indexOf('--dir');
-  const brainDir = (dirIdx >= 0 && dirIdx + 1 < args.length) ? args[dirIdx + 1] : '.';
+  const explicitDir = dirIdx >= 0 && dirIdx + 1 < args.length;
+  // When --dir is not passed, resolve from the configured brain source
+  // BEFORE falling back to '.' (the prior default). The bare `.` default was
+  // a footgun: a user who runs `gbrain extract links` from anywhere outside
+  // their brain dir (e.g., a project checkout with a node_modules tree) had
+  // the recursive walker grab tens of thousands of unrelated .md files,
+  // attempt to extract links between them, then write 0 rows because the
+  // synthetic from_slugs don't match any pages row. The output ("created 0
+  // links from 28989 pages") looks like a no-op, but it walked 28K junk files
+  // first. Resolving from sources(local_path) makes the no-arg invocation
+  // match what `gbrain sync` already does, and keeps cwd-cwd usage available
+  // via explicit `--dir .`.
+  let brainDir = explicitDir ? args[dirIdx + 1] : '.';
   const sourceIdx = args.indexOf('--source');
   const source = (sourceIdx >= 0 && sourceIdx + 1 < args.length) ? args[sourceIdx + 1] : 'fs';
   const typeIdx = args.indexOf('--type');
@@ -390,7 +402,25 @@ export async function runExtract(engine: BrainEngine, args: string[]) {
     process.exit(1);
   }
 
-  // FS source needs a brain dir; DB source ignores --dir.
+  // FS source needs a brain dir. When --dir wasn't passed, resolve from
+  // sources(local_path) — same path `gbrain sync` uses — instead of
+  // silently walking cwd. See the brainDir comment above for the footgun.
+  if (source === 'fs' && !explicitDir) {
+    const { getDefaultSourcePath } = await import('../core/source-resolver.ts');
+    const configured = await getDefaultSourcePath(engine);
+    if (configured) {
+      brainDir = configured;
+    } else {
+      console.error(
+        `No brain directory configured. Pass --dir <path> explicitly, or use --source db ` +
+        `to extract from already-synced pages. To register a brain dir as the default, ` +
+        `run: gbrain sources add default --path <brain-dir>`,
+      );
+      process.exit(1);
+    }
+  }
+
+  // DB source ignores --dir.
   if (source === 'fs' && !existsSync(brainDir)) {
     console.error(`Directory not found: ${brainDir}`);
     process.exit(1);

test/extract-fs.test.ts

@@ -159,3 +159,90 @@ title: Alice
     expect(elapsedMs).toBeLessThan(2000);
   });
 });
+
+describe('gbrain extract --dir default resolution', () => {
+  // Pin the cwd-footgun fix: when --dir is not passed, extract resolves the
+  // brain dir from the sources(local_path) row before falling back. The bare
+  // `.` default would let a user running from a directory with a node_modules/
+  // tree walk tens of thousands of unrelated .md files and report
+  // "created 0 links from 28K pages" — looks like a no-op, was actually a
+  // wasteful junk walk that wrote nothing because synthetic from_slugs don't
+  // match the pages table.
+  test('uses configured sources(local_path) when --dir is not passed', async () => {
+    await engine.putPage('people/alice', personPage('Alice'));
+    await engine.putPage('people/bob', personPage('Bob'));
+    writeFile('people/alice.md', '---\ntitle: Alice\n---\n\n[Bob](../people/bob.md) is a friend.\n');
+    writeFile('people/bob.md', '---\ntitle: Bob\n---\n');
+
+    // Register brainDir as the default source's local_path.
+    await (engine as any).db.exec(
+      `UPDATE sources SET local_path = '${brainDir.replace(/'/g, "''")}' WHERE id = 'default'`,
+    );
+
+    // Save + clobber cwd to a sibling tmpdir so the test fails loudly if the
+    // resolver still walks `.` instead of the configured path.
+    const otherDir = mkdtempSync(join(tmpdir(), 'gbrain-extract-other-'));
+    const savedCwd = process.cwd();
+    try {
+      process.chdir(otherDir);
+      await runExtract(engine, ['links']); // no --dir
+    } finally {
+      process.chdir(savedCwd);
+      try { rmSync(otherDir, { recursive: true, force: true }); } catch { /* ignore */ }
+    }
+
+    const links = await engine.getLinks('people/alice');
+    expect(links.length).toBe(1);
+    expect(links[0]).toMatchObject({ to_slug: 'people/bob' });
+  });
+
+  test('errors with actionable message when no --dir and no source configured', async () => {
+    // Clear the default source's local_path so getDefaultSourcePath returns null.
+    await (engine as any).db.exec(`UPDATE sources SET local_path = NULL WHERE id = 'default'`);
+    await (engine as any).db.exec(`DELETE FROM config WHERE key = 'sync.repo_path'`);
+
+    let exitCode: number | null = null;
+    const errBuf: string[] = [];
+    const savedExit = process.exit;
+    const savedConsoleError = console.error;
+    try {
+      (process as any).exit = (code: number) => { exitCode = code; throw new Error('__test_exit__'); };
+      console.error = (...parts: unknown[]) => { errBuf.push(parts.join(' ')); };
+      try {
+        await runExtract(engine, ['links']);
+      } catch (e) {
+        if (!(e instanceof Error && e.message === '__test_exit__')) throw e;
+      }
+    } finally {
+      (process as any).exit = savedExit;
+      console.error = savedConsoleError;
+    }
+    expect(exitCode).toBe(1);
+    const all = errBuf.join('\n');
+    expect(all).toContain('No brain directory configured');
+    expect(all).toContain('--source db');
+    expect(all).toContain('--dir');
+  });
+
+  test('explicit --dir always wins over configured source', async () => {
+    await engine.putPage('people/alice', personPage('Alice'));
+    await engine.putPage('people/bob', personPage('Bob'));
+    writeFile('people/alice.md', '---\ntitle: Alice\n---\n\n[Bob](../people/bob.md) is a friend.\n');
+    writeFile('people/bob.md', '---\ntitle: Bob\n---\n');
+
+    // Configured path points elsewhere; explicit --dir must override.
+    const decoyDir = mkdtempSync(join(tmpdir(), 'gbrain-extract-decoy-'));
+    await (engine as any).db.exec(
+      `UPDATE sources SET local_path = '${decoyDir.replace(/'/g, "''")}' WHERE id = 'default'`,
+    );
+
+    try {
+      await runExtract(engine, ['links', '--dir', brainDir]);
+      const links = await engine.getLinks('people/alice');
+      expect(links.length).toBe(1);
+      expect(links[0]).toMatchObject({ to_slug: 'people/bob' });
+    } finally {
+      try { rmSync(decoyDir, { recursive: true, force: true }); } catch { /* ignore */ }
+    }
+  });
+});