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.