fix: detect stale registry and reinstall git extension when directory missing

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
Agent-Logs-Url: https://github.com/github/spec-kit/sessions/d5cbfcf4-4651-4784-9234-c4a42a333438

Author: Copilot

src/specify_cli/__init__.py

@@ -1199,9 +1199,15 @@ def _install_bundled_git_extension(project_path: Path) -> bool:
         from .extensions import ExtensionManager
         manager = ExtensionManager(project_path)
 
-        # Skip if already installed (e.g. via preset)
+        # Skip if already installed (e.g. via preset), but only if the
+        # on-disk extension manifest still exists. This guards against
+        # stale/corrupted registry entries.
         if manager.registry.is_installed("git"):
-            return True
+            ext_manifest = project_path / ".specify" / "extensions" / "git" / "extension.yml"
+            if ext_manifest.is_file():
+                return True
+            # Registry is stale — remove entry so reinstall can proceed
+            manager.registry.remove("git")
 
         speckit_ver = get_speckit_version()
         manager.install_from_directory(ext_source, speckit_ver)

tests/test_branch_numbering.py

@@ -138,3 +138,33 @@ def test_git_extension_noop_when_already_installed(self, tmp_path: Path):
         # Only one entry in registry
         manager = ExtensionManager(project_dir)
         assert manager.registry.is_installed("git")
+
+    def test_git_extension_reinstalls_when_directory_missing(self, tmp_path: Path):
+        """_install_bundled_git_extension should reinstall if registry says installed but directory is gone."""
+        import shutil
+        from specify_cli import _install_bundled_git_extension
+        from specify_cli.extensions import ExtensionManager
+
+        project_dir = tmp_path / "proj"
+        (project_dir / ".specify").mkdir(parents=True)
+
+        # First install
+        result1 = _install_bundled_git_extension(project_dir)
+        assert result1 is True
+
+        ext_dir = project_dir / ".specify" / "extensions" / "git"
+        assert ext_dir.is_dir()
+
+        # Simulate stale registry: delete extension directory but keep registry
+        shutil.rmtree(ext_dir)
+        assert not ext_dir.exists()
+
+        # Registry still says installed
+        manager = ExtensionManager(project_dir)
+        assert manager.registry.is_installed("git")
+
+        # Re-install should detect missing directory and reinstall
+        result2 = _install_bundled_git_extension(project_dir)
+        assert result2 is True
+        assert ext_dir.is_dir(), "extension directory should be reinstalled"
+        assert (ext_dir / "extension.yml").is_file(), "extension.yml should be reinstalled"