Also Meta is actively encouraging users to grant them full permission, insisting with all their marketing might that it’s safe, which they know is a complete lie. Hard to blame the user when they’re being actively deceived like this. Other agent companies are more reserved and say things like “be careful” but Meta is the opposite.
As for security models, it's probably long since time to sandbox all data and apps. More like mobile devices. Allow users to toggle that all off so they can use their computers for development etc, but the default state should force apps/tools to explicitly ask for permission to any folder, other app, API, CLI, etc. And ask for that permission regularly (or rather, reset the permission after some period of time). Or something like that (I haven't given it a great amount of thought).