The permission thing is a killer to productivity, if you're running Claude I think it's more efficient to just run in a disposable sandbox (like exe.dev[1]) or in some form of docker container with permissions you're personally ok taking the risk with on a personal machine[2]
[1] - https://exe.dev/ is a new cloud provider with some very useful agent UX [2] - I built https://github.com/stanislavkozlovski/dclaude/ for this; not perfect but gets my job done on the rare occassion I need to run the coding agent locally
A disposable sandbox wont protect you from secret exfiltration. Assuming you don't consider your code a secret, you could of course set up your sandbox so it doesn't have any secrets, but that would severely limit the kinds of tasks you can use the agent for.