fix(extraction): detect untracked files inside untracked directories (#1213) (#1215)

git status --porcelain collapses an entirely-untracked directory into a
single '?? dir/' entry. collectGitStatus only recurses into such dirs to
find embedded git repos, so source files in a plain untracked directory
were never surfaced to sync — 'codegraph sync' reported 'Already up to
date' and the watcher missed them too.

Add -uall so git lists individual untracked files. Nested untracked git
repos still collapse to '?? repo/' even with -uall (git never crosses a
repo boundary), so the embedded-repo recursion is unaffected.

Export getGitChangedFiles and add regression tests for both the plain
untracked-directory case and the embedded-repo recursion (no -uall
regression).

Root-cause analysis and fix suggested by the reporter in #1213.

src/extraction/index.ts

@@ -1104,7 +1104,7 @@ interface GitChanges {
  * case this cannot see (the child status that would report the deletions is gone
  * with it); a full `codegraph index` reconciles that.
  */
-function getGitChangedFiles(rootDir: string): GitChanges | null {
+export function getGitChangedFiles(rootDir: string): GitChanges | null {
   try {
     const changes: GitChanges = { modified: [], added: [], deleted: [] };
     // Custom extension → language overrides from the project's codegraph.json,
@@ -1120,7 +1120,13 @@ function getGitChangedFiles(rootDir: string): GitChanges | null {
 function collectGitStatus(repoDir: string, prefix: string, out: GitChanges, overrides?: Record<string, Language>, includeIgnored: Ignore | null = null, exclude: Ignore | null = null): void {
   const output = execFileSync(
     'git',
-    ['status', '--porcelain', '--no-renames'],
+    // `-uall` lists individual untracked files instead of collapsing an
+    // entirely-untracked directory into one `?? dir/` entry, which would
+    // otherwise be dropped here (only embedded git repos are recursed into
+    // below). Nested untracked git repos still collapse to `?? repo/` even
+    // with `-uall` — git never crosses a repo boundary — so the recursion
+    // still handles them. (#1213)
+    ['status', '--porcelain', '--no-renames', '-uall'],
     { cwd: repoDir, encoding: 'utf-8', timeout: 10000, maxBuffer: 50 * 1024 * 1024, stdio: ['pipe', 'pipe', 'pipe'], windowsHide: true }
   );