It nuked a substantial portion of the file, unfortunately, not just the comments. It basically gave me a reset config.toml with your MCP and not too much else.

I have a nontrivial config. Will share on your Issues page when I can.

Appreciate it. An anonymized repro file would help ensure we validate against your specific cases.

Closing loop - we merged in a PR that lifted the codex toml modification logic from the codex source code, so it should be safe to use. We weren't able to recreate cases were the previous approach broke our test cases, but by porting codex logic we figure is the best way to structurally ensure there aren't unforseen changes.

If you run into any other issues -- let us know.