Since Astra (medium) I catch agents responding that they changed files and yet I see no diffs. Turns out that’s because they use python scripts in bash to edit files. I assume that apply_patch passes changes to diff viewer functionality and that’s the root cause. Screenshot is from GUI but cli behaves the same way.
I’d first check git status and git diff from the same repository. If Git shows the Python script’s changes correctly but Codex shows no diff, that strongly points to the Codex UI/review layer. On Windows, there have also been cases where Codex constructed the Git path incorrectly, causing diffs to fail.
A useful workaround for now is to verify the changes with git diff after the script runs and restart/reload the Codex review view. It would be good for Codex to handle externally modified files more reliably, especially since Python scripts and formatters commonly modify files outside the agent’s direct edit flow.