WIP: Clean up usage of shutil.rmtree()

Description

This cleans up all problematic invocations of shutil.rmtree documented as part of #1171 (closed), except for the one in src/buildstream/sandbox/_sandboxbwrap.py:312: shutil.rmtree(base_directory, ignore_errors=True).

This last one is more tricky to work around, ideally we should write a message to the user telling them that we left debris, but we don't have access to a messenger here. This will be obsoleted once we start using buildbox-run for bwrap anyway, so it's not really worth the effort of changing the sandboxing API for that.

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