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Changes the default behaviour of the Python extractor so files inside hidden directories are extracted by default. Also adds an extractor option, `skip_hidden_directories`, which can be set to `true` in order to revert to the old behaviour. Finally, I made the logic surrounding what is logged in various cases a bit more obvious. Technically this changes the behaviour of the extractor (in that hidden excluded files will now be logged as `(excluded)`, but I think this makes more sense anyway.