Does containerization help much here? If it's a code tool then presumably it needs access to your code files (read / write). Maybe there are use cases for it of course.

WASI provides a very nice mental model where you can mount, e.g., /input, as read-only, and where every mutation is saved in /output or what-not. At least that's my favorite contract: input files remain untouched, but we can copy them and do whatever we want with them in /scratch or /output (which the user can later investigate and make sure nothing went horribly wrong while still having backups).