fix(extensions): preserve-capture only from a real dir; reset non-dir dest_dir in main path

Two more symlink-safety fixes to the keep-config reinstall:

1. The preserved-config capture guarded on dest_dir.exists(), which is true for a
   symlink; iterating a symlinked dest_dir would follow the link and read
   arbitrary external files into preserved_configs. Require a real directory
   (is_dir() and not is_symlink()) so only genuine on-disk leftover configs are
   captured.

2. The main install path cleared dest_dir with shutil.rmtree(dest_dir), which
   raises on a symlink or file (NotADirectoryError) and didn't benefit from the
   _reset_dir behavior already used in rollback. Use self._reset_dir(dest_dir) so
   an unexpected occupant (symlink/file) is handled consistently instead of
   crashing on path type.

Tests: a stray FILE at dest_dir is replaced cleanly (cross-platform; fails before
with NotADirectoryError), and the capture ignores a symlinked dest_dir without
reading/overwriting external files (skipped without symlink privilege, runs on CI).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: jawwad-ali

src/specify_cli/extensions/__init__.py

@@ -1519,7 +1519,11 @@ def install_from_directory(
         # secrets (API keys); recreating them with default perms could widen
         # access.
         preserved_configs: dict[str, tuple[bytes, int, float, float]] = {}
-        if dest_dir.exists():
+        # Require a REAL directory, not a symlink: iterating a symlinked dest_dir
+        # would follow the link and read arbitrary external files into
+        # preserved_configs. This path only ever legitimately captures on-disk
+        # leftover configs inside the real extension directory.
+        if dest_dir.is_dir() and not dest_dir.is_symlink():
             for cfg_file in dest_dir.iterdir():
                 if (
                     cfg_file.is_file()
@@ -1561,8 +1565,10 @@ def install_from_directory(
 
         restored_ok = not preserved_configs
         try:
-            if dest_dir.exists():
-                shutil.rmtree(dest_dir)
+            # Reset via _reset_dir (unlink a symlink / rmtree a real dir) rather
+            # than a bare rmtree, which raises on a symlink or file at dest_dir.
+            # Handles an unexpected occupant consistently with the rollback path.
+            self._reset_dir(dest_dir)
             shutil.copytree(source_dir, dest_dir, ignore=ignore_fn)
             # Restore every preserved config. A failure here is NOT swallowed: a
             # config we promised to preserve but could not restore must fail the

tests/test_extensions.py

@@ -1870,6 +1870,63 @@ def copytree_symlinks_destdir_first(src, dst, *args, **kwargs):
         assert config_file.is_file()
         assert "SECRET-VALUE" in config_file.read_text()
 
+    def test_reinstall_replaces_file_at_dest_dir(self, extension_dir, project_dir):
+        """If a non-directory (a stray file) occupies dest_dir at reinstall, the
+        main install path clears it via _reset_dir rather than crashing on
+        shutil.rmtree (which raises NotADirectoryError on a file)."""
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        # Drop the registry entry, then replace the extension dir with a file.
+        assert manager.remove("test-ext", keep_config=True) is True
+        shutil.rmtree(ext_dir)
+        ext_dir.write_text("not a directory")
+        assert ext_dir.is_file()
+
+        # Reinstall must succeed, replacing the file with a real extension dir.
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+        assert ext_dir.is_dir() and not ext_dir.is_symlink()
+        assert (ext_dir / "extension.yml").is_file()
+
+    def test_preserve_capture_ignores_symlinked_dest_dir(
+        self, extension_dir, project_dir
+    ):
+        """The preserve-config capture must not follow a symlinked dest_dir and
+        read external files into preserved_configs. Skipped without symlink
+        privilege; runs on Linux CI."""
+        probe_t = project_dir / "_pt2"
+        probe_l = project_dir / "_pl2"
+        try:
+            probe_t.mkdir()
+            probe_l.symlink_to(probe_t, target_is_directory=True)
+        except (OSError, NotImplementedError):
+            pytest.skip("symlinks not supported in this environment")
+        finally:
+            if probe_l.is_symlink():
+                probe_l.unlink()
+            if probe_t.exists():
+                shutil.rmtree(probe_t, ignore_errors=True)
+
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        assert manager.remove("test-ext", keep_config=True) is True
+
+        # External dir with a config-looking file that must NOT be captured.
+        external = project_dir / "external_configs"
+        external.mkdir()
+        (external / "test-ext-config.yml").write_text("api_key: EXTERNAL-SECRET")
+        # Swap dest_dir for a symlink to the external dir.
+        shutil.rmtree(ext_dir)
+        ext_dir.symlink_to(external, target_is_directory=True)
+
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # The external secret was never captured, restored, or overwritten.
+        assert (external / "test-ext-config.yml").read_text() == "api_key: EXTERNAL-SECRET"
+        assert ext_dir.is_dir() and not ext_dir.is_symlink()
+        assert not (ext_dir / "test-ext-config.yml").exists()
+
 
 # ===== CommandRegistrar Tests =====