fix: tolerate post-commit preset cleanup failures

Keep successful preset updates successful when backup or staging cleanup cannot remove a recovery artifact, while warning with the retained path.

Assisted-by: GitHub Copilot (model: gpt-5.6-luna, autonomous)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Copilot-Session: 1782a274-fe10-44b1-b5b7-65a5f13cdc27

Author: digimangos

src/specify_cli/presets/__init__.py

@@ -4383,12 +4383,27 @@ def _update_from_directory_locked(
         os.rmdir(swap_token)
         staging_dir = Path(f"{swap_token}.staging")
         backup_dir = Path(f"{swap_token}.bak")
+
         def remove_swap_path(path: Path) -> None:
             if path.is_symlink():
                 path.unlink()
             elif path.exists():
                 shutil.rmtree(path)
 
+        def remove_committed_swap_path(path: Path, artifact_kind: str) -> None:
+            try:
+                remove_swap_path(path)
+            except OSError as exc:
+                import warnings
+
+                warnings.warn(
+                    f"Preset '{target_id}' was updated successfully, but its "
+                    f"temporary {artifact_kind} path could not be removed: "
+                    f"{path} ({exc}). Inspect and remove this recovery "
+                    "artifact manually once it is safe to do so.",
+                    stacklevel=2,
+                )
+
         def ignore_staging_state(directory: str, names: List[str]) -> Set[str]:
             directory_path = Path(directory)
             return {
@@ -4470,8 +4485,8 @@ def ignore_staging_state(directory: str, names: List[str]) -> Set[str]:
             # provenance until removal. Updating only replaces the source and
             # metadata while retaining enough ownership data for a later
             # removal to clean up artifacts left on disk.
-            remove_swap_path(backup_dir)
-            remove_swap_path(staging_dir)
+            remove_committed_swap_path(backup_dir, "backup")
+            remove_committed_swap_path(staging_dir, "staging")
             return new_manifest, diff
 
         primary_command_names = {
@@ -4810,8 +4825,8 @@ def _preset_has_constitution_layer(
                 stacklevel=2,
             )
         finally:
-            remove_swap_path(backup_dir)
-            remove_swap_path(staging_dir)
+            remove_committed_swap_path(backup_dir, "backup")
+            remove_committed_swap_path(staging_dir, "staging")
         return new_manifest, diff
 
     def update_from_archive(

tests/test_presets.py

@@ -15617,6 +15617,51 @@ def test_update_preserves_priority_and_enabled_state(
         assert metadata["enabled"] is False
         assert (project_dir / ".specify/presets/test-pack/preset.yml").exists()
 
+    @pytest.mark.parametrize("enabled", [False, True])
+    def test_post_commit_backup_cleanup_failure_warns_without_failing_update(
+        self, project_dir, pack_dir, monkeypatch, enabled
+    ):
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(pack_dir, "0.1.0")
+        if not enabled:
+            manager.registry.update("test-pack", {"enabled": False})
+        source = self._updated_source(pack_dir)
+        original_rmtree = shutil.rmtree
+
+        def fail_committed_backup(path, *args, **kwargs):
+            if Path(path).name.startswith(".test-pack.update-") and Path(
+                path
+            ).name.endswith(".bak"):
+                raise PermissionError("simulated committed backup cleanup failure")
+            return original_rmtree(path, *args, **kwargs)
+
+        monkeypatch.setattr(shutil, "rmtree", fail_committed_backup)
+
+        with pytest.warns(UserWarning, match="updated successfully") as caught:
+            manifest, diff = manager.update_from_directory(
+                source, "0.1.0", pack_id="test-pack"
+            )
+
+        assert manifest.version == "2.0.0"
+        assert diff["added"]
+        metadata = manager.registry.get("test-pack")
+        assert metadata["version"] == "2.0.0"
+        assert metadata["enabled"] is enabled
+        assert "2.0.0" in (
+            project_dir / ".specify/presets/test-pack/preset.yml"
+        ).read_text(encoding="utf-8")
+        backups = list(
+            (project_dir / ".specify/presets").glob(
+                ".test-pack.update-*.bak"
+            )
+        )
+        assert len(backups) == 1
+        warning = str(caught[0].message)
+        assert "temporary backup path" in warning
+        assert str(backups[0]) in warning
+        assert "Inspect and remove this recovery artifact" in warning
+        original_rmtree(backups[0])
+
     def test_dry_run_does_not_modify_installation(self, project_dir, pack_dir):
         manager = PresetManager(project_dir)
         manager.install_from_directory(pack_dir, "0.1.0", priority=4)
@@ -16962,6 +17007,42 @@ def test_cli_bulk_confirms_once_for_multiple_presets(
         assert registry.get("test-pack")["version"] == "2.0.0"
         assert registry.get("second-pack")["version"] == "2.0.0"
 
+    def test_cli_bulk_cleanup_warning_does_not_report_successful_update_as_failed(
+        self, project_dir, pack_dir, monkeypatch
+    ):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        self._two_actionable_packs(project_dir, pack_dir, monkeypatch)
+        original_rmtree = shutil.rmtree
+
+        def fail_first_committed_backup(path, *args, **kwargs):
+            name = Path(path).name
+            if name.startswith(".test-pack.update-") and name.endswith(".bak"):
+                raise PermissionError("simulated committed backup cleanup failure")
+            return original_rmtree(path, *args, **kwargs)
+
+        monkeypatch.setattr(shutil, "rmtree", fail_first_committed_backup)
+
+        with pytest.warns(UserWarning, match="updated successfully") as caught:
+            result = CliRunner().invoke(app, ["preset", "update"], input="y\n")
+
+        assert result.exit_code == 0, result.output
+        assert "test-pack: updated" in result.output
+        assert "second-pack: updated" in result.output
+        assert "failed" not in result.output
+        registry = PresetManager(project_dir).registry
+        assert registry.get("test-pack")["version"] == "2.0.0"
+        assert registry.get("second-pack")["version"] == "2.0.0"
+        backups = list(
+            (project_dir / ".specify/presets").glob(
+                ".test-pack.update-*.bak"
+            )
+        )
+        assert len(backups) == 1
+        assert str(backups[0]) in str(caught[0].message)
+        original_rmtree(backups[0])
+
     def test_cli_all_flag_matches_bare_bulk_invocation(
         self, project_dir, pack_dir, monkeypatch
     ):