Yeah, spot on. I had an agent delete some files it shouldn't have as well, similarly to me making the same mistake. I think system prompts should default to using `trash` over `rm`. For now that's just in my AGENTS.md, and gets honored most of the time.
You can always use something like this [1], which will make sure any file removed on the command line via rm (or other utilities, like git rm) ends up in the trash instead
[1] https://github.com/faratech/trashd