I faced a similar issue. I used codex inside VS code with full access and the prompt I used contained the following sentences that could have caused the issue
“Clean repository packaging and ignore rules so generated/runtime junk is not part of normal source control flow.”
- “Part 2: Clean generated/source-control junk”
- “Inspect the repo and clean source-control hygiene.”
- “At minimum, address things like … build outputs … local storage/runtime artifacts that should not be committed”
- “remove generated artifacts from tracked source if they are present in the working tree”