Overwrite existing files when hardlinking (#402)
## Summary
Closes https://github.com/astral-sh/puffin/issues/390.
## Test Plan
Installed `jupyter_core==5.5.0`, then removed the `jupyter_core` and
`jupyter_core-5.5.0.dist-info` directories from my virtualenv manually,
but left `jupyter.py`. I then re-ran `puffin pip-compile`, and verified
that it errored on `main` but succeeded here.
