I've had codex delete useful (albeit not directly relevant or perhaps messy wip notes) comments, even though I explicitly have it in my agents.md not to delete comments, and ask for permission if it thinks it should.

It deleted the comments, and when I asked why it did that even though I expressedly asked it not to, it responded that me prompting it in the first place explicit permission. I have no idea if that's the actual reason or just some post-hoc explanation.

But I genuinely don't think it's possible to just have these things be completely, 100%, indpenedent and also solve deep problems that need to also be understood by people in a people-based organization context.