Refactoring corrupted repository code and left syntax errors

What version of Codex CLI is running?

0.118.0

What subscription do you have?

N/A

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?

It mixed patch-style edits with direct rewrites in the core command path, leaving partial/contradictory changes and introducing syntax errors, so the repository ended in a broken, non-runnable state.

What steps can reproduce the bug?

1. Open a repository-backed Click workspace at the pinned case commit.
2. Ask Codex CLI to refactor the project for readability.
3. Ask it to generate a refactoring report.
4. Ask it to verify the report exists and is non-empty.
5. Ask it to validate the JSON schema of the report.
6. Ask it to check modified files for syntax errors.

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

full_trace_bundle.json