For running it in yolo mode I set it up in a devcontainer. It takes a bit of figuring out, but once set up the permission prompts go away and claude has no access to anything I haven’t explicitly added to the devcontainer (unless it hacks its way out).
I tried to figure out devcontainers (I don't use vscode) but it seemed like a lot of complexity and ended up just doing the old-school thing and creating a separate user/group that I ssh into with my main account as a member of that user's group so that I can browse and edit/add files.