fix(sync): filter git-status fast path through ignore matcher

__tests__/sync.test.ts

@@ -302,5 +302,37 @@ describe('Sync Module', () => {
       expect(result.filesRemoved).toBe(0);
       expect(result.changedFilePaths).toBeUndefined();
     });
+
+    it('should not index tracked files in default-ignored dirs (issue #766)', async () => {
+      // Create a committed file inside node_modules/ (a default-ignored dir).
+      // git status reports changes to tracked files even when they match
+      // DEFAULT_IGNORE_PATTERNS — the sync git fast path must filter them.
+      const nmDir = path.join(testDir, 'node_modules', 'pkg');
+      fs.mkdirSync(nmDir, { recursive: true });
+      fs.writeFileSync(
+        path.join(nmDir, 'index.ts'),
+        `export function depFunc() { return 'original'; }`
+      );
+      git('add', '-A');
+      git('commit', '-m', 'add dependency');
+
+      // Full index excludes node_modules/ — depFunc is NOT in the graph.
+      await cg.indexAll();
+      expect(cg.searchNodes('depFunc').length).toBe(0);
+
+      // Modify the tracked file inside node_modules/.
+      fs.writeFileSync(
+        path.join(nmDir, 'index.ts'),
+        `export function depFunc() { return 'modified'; }`
+      );
+
+      // sync() must NOT pick up the change — the file is in an ignored dir.
+      const result = await cg.sync();
+      expect(result.filesAdded).toBe(0);
+      expect(result.filesModified).toBe(0);
+
+      // depFunc is still not in the graph.
+      expect(cg.searchNodes('depFunc').length).toBe(0);
+    });
   });
 });

src/extraction/index.ts

@@ -1810,7 +1810,15 @@ export class ExtractionOrchestrator {
       // files stay untracked in git even after indexing, so they must be
       // hash-compared like modified files instead of always counting as added —
       // otherwise status reports them as pending forever. (See issue #206.)
+      //
+      // Filter through the same ignore matcher used by getGitVisibleFiles so
+      // tracked files in excluded dirs (e.g. a committed `vendor/`) don't leak
+      // back into the index. git status reports changes to tracked files even
+      // when they match DEFAULT_IGNORE_PATTERNS or a .gitignore entry. (#766)
+      const ig = buildDefaultIgnore(this.rootDir);
       for (const filePath of [...gitChanges.modified, ...gitChanges.added]) {
+        if (ig.ignores(filePath)) continue;
+
         const fullPath = path.join(this.rootDir, filePath);
         let content: string;
         try {