I could ask this question without AI. How are you going to notice that while you were working on ~/projects/acme3000, you for some reason deleted ~/photos/2003/once-in-a-lifetime-holiday/?
Of course, AI is not a real person, and it does make mistakes that you or I probably would not. However, this class of mistake—deleting completely unrelated directories—does not appear to be a common failure mode. (Something like deleting all of ~ doesn’t count here—that would be immediately noticeable and could be restored from a backup.)
(Disclaimer, I’m not OP and I wouldn’t run Claude with —-dangerously-skip-permissions on my own system)
Isn't the problem that of finding out a consistency heuristic? For example, test that the resulting state is consistent with your test suite.
If it is a directory that gets deleted, then you can diff it with a previous state. If you don't control the state and don't know the surface area that you should observe, then yes, you're inviting trouble if agents run amok.
Backups are great when you know you need to restore.