fix(extraction): index independent nested git repos

__tests__/extraction.test.ts

@@ -3130,6 +3130,37 @@ describe('Git Submodules', () => {
     expect(files).toContain('app.ts');
     expect(files).toContain('libs/lib/lib.ts');
   });
+
+  it('should index files inside independent nested git repositories (issue #193)', async () => {
+    const { execFileSync } = await import('child_process');
+    const git = (cwd: string, ...args: string[]) =>
+      execFileSync('git', args, { cwd, stdio: 'pipe' });
+
+    const mainDir = path.join(tempDir, 'main');
+    fs.mkdirSync(mainDir, { recursive: true });
+    git(mainDir, 'init', '-q');
+    git(mainDir, 'config', 'user.email', 'test@test.com');
+    git(mainDir, 'config', 'user.name', 'Test');
+    fs.writeFileSync(path.join(mainDir, 'CMakeLists.txt'), 'add_subdirectory(sub_repo1)\n');
+    git(mainDir, 'add', 'CMakeLists.txt');
+    git(mainDir, 'commit', '-q', '-m', 'root init');
+
+    const nestedRepo = path.join(mainDir, 'sub_repo1');
+    fs.mkdirSync(path.join(nestedRepo, 'src'), { recursive: true });
+    git(nestedRepo, 'init', '-q');
+    git(nestedRepo, 'config', 'user.email', 'test@test.com');
+    git(nestedRepo, 'config', 'user.name', 'Test');
+    fs.writeFileSync(path.join(nestedRepo, 'CMakeLists.txt'), 'project(sub_repo1)\n');
+    fs.writeFileSync(path.join(nestedRepo, 'src', 'main.cpp'), 'int main() { return 0; }\n');
+    git(nestedRepo, 'add', '-A');
+    git(nestedRepo, 'commit', '-q', '-m', 'nested init');
+
+    const config = { ...DEFAULT_CONFIG, rootDir: mainDir };
+    const files = scanDirectory(mainDir, config);
+
+    expect(files).toContain('sub_repo1/src/main.cpp');
+    expect(files.every((file) => !file.includes('.git/'))).toBe(true);
+  });
 });
 
 // =============================================================================

src/extraction/index.ts

@@ -101,6 +101,14 @@ function matchesGlob(filePath: string, pattern: string): boolean {
   return picomatch.isMatch(filePath, pattern, { dot: true });
 }
 
+function isSameDirectory(left: string, right: string): boolean {
+  try {
+    return fs.realpathSync(left) === fs.realpathSync(right);
+  } catch {
+    return path.resolve(left) === path.resolve(right);
+  }
+}
+
 /**
  * Check if a file should be included based on config
  */
@@ -141,7 +149,7 @@ function getGitVisibleFiles(rootDir: string): Set<string> | null {
       { cwd: rootDir, encoding: 'utf-8', timeout: 5000, stdio: ['pipe', 'pipe', 'pipe'] }
     ).trim();
 
-    if (path.resolve(gitRoot) !== path.resolve(rootDir)) {
+    if (!isSameDirectory(gitRoot, rootDir)) {
       try {
         // git check-ignore exits 0 if the path IS ignored, 1 if not
         execFileSync(
@@ -177,7 +185,20 @@ function getGitVisibleFiles(rootDir: string): Set<string> | null {
     for (const line of untracked.split('\n')) {
       const trimmed = line.trim();
       if (trimmed) {
-        files.add(normalizePath(trimmed));
+        const normalized = normalizePath(trimmed);
+        // Git reports unregistered nested repos as "dir/" entries; expand
+        // them so top-level workspace indexes can see the repo's files.
+        if (normalized.endsWith('/')) {
+          const nestedFiles = getNestedGitRepoFiles(rootDir, normalized);
+          if (nestedFiles.length > 0) {
+            for (const nestedFile of nestedFiles) {
+              files.add(nestedFile);
+            }
+            continue;
+          }
+        }
+
+        files.add(normalized);
       }
     }
 
@@ -244,6 +265,38 @@ function getGitChangedFiles(rootDir: string, config: CodeGraphConfig): GitChange
  */
 const CODEGRAPH_IGNORE_MARKER = '.codegraphignore';
 
+function isGitRepositoryRoot(dir: string): boolean {
+  try {
+    const gitRoot = execFileSync(
+      'git',
+      ['rev-parse', '--show-toplevel'],
+      { cwd: dir, encoding: 'utf-8', timeout: 5000, stdio: ['pipe', 'pipe', 'pipe'] }
+    ).trim();
+    return isSameDirectory(gitRoot, dir);
+  } catch {
+    return false;
+  }
+}
+
+function getNestedGitRepoFiles(rootDir: string, nestedRelativePath: string): string[] {
+  const nestedPrefix = normalizePath(nestedRelativePath).replace(/\/+$/, '');
+  if (!nestedPrefix) return [];
+
+  const nestedRoot = path.join(rootDir, nestedPrefix);
+  try {
+    if (!fs.statSync(nestedRoot).isDirectory()) return [];
+  } catch {
+    return [];
+  }
+
+  if (!isGitRepositoryRoot(nestedRoot)) return [];
+
+  const nestedFiles = getGitVisibleFiles(nestedRoot);
+  if (!nestedFiles) return [];
+
+  return [...nestedFiles].map((filePath) => normalizePath(path.join(nestedPrefix, filePath)));
+}
+
 /**
  * Recursively scan directory for source files.
  *