Fix secondary runs cleanup issue on windows

[Sun Haoran (haoranpb)]

We clone plugin repos during runtime, the secondary run will have to delete the previously cloned git repo.

On windows this fails due to permission issues: https://stackoverflow.com/questions/1213706/what-user-do-python-scripts-run-as-in-windows.

We had similar problems before in nl2al, move the cleanup logic into operations utilities.

---

In order to catch similar issues in tests, lint and test job now run on both ubuntu and windows

[Copilot]

Pull request overview

Centralizes read-only directory cleanup to support repeated Windows runs.

Changes:

• Adds a reusable remove_tree operation.
• Uses it for repository cloning and NL2AL cleanup.
• Extends clone cleanup testing with a read-only file.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_git_operations.py	Adds read-only clone cleanup coverage.
src/bcbench/operations/git_operations.py	Uses centralized cleanup before cloning.
src/bcbench/operations/filesystem_operations.py	Implements read-only tree removal.
src/bcbench/operations/__init__.py	Exports the new operation.
src/bcbench/evaluate/nl2al.py	Reuses centralized cleanup logic.

[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

tests/test_git_operations.py:240

• This does not exercise the Windows-specific recovery path in CI. On Ubuntu, a read-only file can still be unlinked from a writable parent, so this test also passes with the previous plain shutil.rmtree; the repository's pytest job runs only on ubuntu-latest (.github/workflows/CI.yml:18). Add a Windows test job or a platform-independent test that forces rmtree to invoke the onexc callback, otherwise the regression fix remains unverified.

    stale_file.chmod(0o444)

[Copilot]

Pull request overview

Copilot reviewed 6 out of 6 changed files in this pull request and generated no new comments.