Add `--ignore-dirs` or similar to `extract`

[akx]

See #53, #253, #401, #124.

Implementation idea:

• Add directory_filter callable arg to extract_from_dir(); this would be used instead of the hard-coded if subdir.startswith('.') or subdir.startswith('_'):
• Generate a directory filter callable from an --ignore-dirs argument, if passed in the CLI

[rlam3]

Looking forward to this patch to ignore certain directories/subdirectories.