prime cleanup needs to be robust and warn about inconsistencies

A simple way to handle this issue would be to warn the user about inconsistencies (e.g. primed or staged files manually deleted from another part) and ignore the missing file instead of halting and catching fire. Handling of inconsistent directories need a bit of attention however since it might be simply missing, or incorrectly populated -- so catch appropriate exceptions to issue warnings accordingly.

I ran a few tests simulating a number of inconsistent scenarios (file missing, directory missing, and file manually added to existing directory in override-prime). File and directory missing are now handled with a warning message, and no special handling is necessary for manually added files (clean part already handles it correctly and doesn't raise an exception on os.rmdir(), as I originally thought). Will add the regression tests and issue a PR.

Fix proposed: https://github.com/snapcore/snapcraft/pull/2450