fix: avoid races in filesystem ops

[lgarrison]

Use exist_ok and missing_ok in pathlib operations where we can.

I didn't do an exhaustive audit of pathlib usage, but I did look at places where the code was using path.exists(). There's still a couple of places with this pattern:

if path.exists():
    shutil.rmtree(path)

I don't think there's an elegant solution that will work across Python versions currently, although in 3.13 I think one can do:

try:
    shutil.rmtree(path)
except FileNotFoundError:
    pass

Because: "Changed in version 3.13: rmtree() now ignores FileNotFoundError exceptions for all but the top-level path." (https://docs.python.org/3.13/library/shutil.html#shutil.rmtree)

Fixes #2279.

[henryiii]

I think this is tripping up a test because we were catching an exception somewhere that has now changed type? (from a quick glance)

[joerick]

This one won't work, because missing_ok was added in Python 3.8, and the repair script runs in the build, so runs on 3.6 and 3.7.