Cleanup step used over-broad workspace move and dismantled repository boundaries

What version of Codex CLI is running?

0.118.0

What subscription do you have?

api call

Which model were you using?

gpt-4o-mini

What platform is your computer?

_No response_

What terminal emulator and version are you using (if applicable)?

WSL2 (Ubuntu 22.04.5 LTS)

What issue are you seeing?

During cleanup, Codex executed an overbroad workspace-level move operation that treated repository content as disposable intermediate files, causing large-scale boundary overreach and repository structure damage.

What steps can reproduce the bug?

1. Open a repository-backed workspace.
2. Ask Codex CLI to perform the requested edit, repair, or cleanup workflow reflected by this report.
3. Observe whether it reproduces the failure described above.

What is the expected behavior?

Codex CLI should either apply a valid change or fail cleanly.
It should not corrupt repository state, write invalid syntax, or perform over-broad filesystem actions.

Additional information

Attached full execution traces from the original run directory

["unexpected file changes: ['.editorconfig', '.gitignore', '.pre-commit-config.yaml', '.readthedocs.yaml', 'CHANGES.rst', 'FETCH_HEAD', 'HEAD', 'LICENSE.txt', 'README', 'README.md']"]

full_trace_bundle.json