With new, granular set of permission rights comes ... a bit of pain.

The problem

After upgrading to OSX Sequoia my terminal of choice - Warp started having weird seemingly permission-like issues. Even simple operations like ls sometimes failed with Operation not permitted (os error 1):

ls /Volumes/BACKUP/
"/Volumes/BACKUP/": Operation not permitted (os error 1)

But other apps like Finder had no problem accessing said folder.

The solution

Eventually I noticed that the issue happened always when I tried to access data on an USB thumb drive. Remembering that apps in newer OSX do not have permission to just access disk willy nilly, I opened: System Settings -> Privacy & Security -> Full Disk Access, changed the toggle for Warp to enabled and let the app reboot. And voila! Now it works again.