Clear ephemeral overlays when running tools (#11141)
## Summary
This PR removes the ephemeral `.pth` overlay when using a cached
environment. This solution isn't _completely_ safe, since we could
remove the `.pth` file just as another process is starting the
environment... But that risk already exists today, since we could
_overwrite_ the `.pth` file just as another process is starting the
environment, so I think what I've added here is a strict improvement.
Ideally, we wouldn't write this file at all, and we'd instead somehow
(e.g.) pass a file to the interpreter to run at startup? Or find some
other solution that doesn't require poisoning the cache like this.
Closes https://github.com/astral-sh/uv/issues/11117.
# Test Plan
Ran through the great reproduction steps from the linked issue.
Before:
After:
