src/setup.py: Disentangle cleaning of stale installed files in build directory and in install directory

[mkoeppe]

This is a follow-up on #21604 (comment 10-12)

[embray]

I think it would be best if this were implemented as an entirely new command--clean_stale, say. Or it could be rolled into the existing clean command. It has a different purpose, but could be done as options to the clean command. #21508 already mentions making the clean command work properly. I've usually found that the built-in setup.py clean command is not always as useful as one would like, so it might be worth extending anyways.