And then one day you want to zip up the project to send to a friend, run an external linter on it, or make backups. ML depends on an adequate training set, and real life uses change quickly enough to break it.

The OS would confirm that it was an end user making the action not malware. It is about the automatic creation of security rules based on observed behavior. The other option would be to create everything manually, which doesn't happen.

Browsers have already taught us how useless this is, users will always click through.

Having an OS that arbitrarily denies applications access to files would drive me mad very quickly. I'm guessing that seemingly unpredictable behaviour would annoy the average user as well.