python: cleaning doesn't remove "old" API directories

If we remove an API path from the config, the now-more-targeted clean operation won't remove the generated code. (It'll remove samples and tests, but not docs and production code.)

Removing a proto from an API should be fine - this is a matter of detecting which directories have previously been generated.

Start with the clean operation for Python APIs and compare how it identifies generated samples and tests versus documentation and production code. Remove an API path or proto from the configuration, then verify that all previously generated directories are cleaned while retained APIs remain.

Written by the indexing model from the issue text.