Skip "root" dirs too

[aulemahal]

Pull Request Checklist:

• This PR addresses an already opened issue (for bug fixes / features)
  • This PR fixes #xyz
• (If applicable) Documentation has been added / updated (for bug fixes / features).
• (If applicable) Tests have been added.
• This PR does not seem to break the templates.
• CHANGELOG.rst has been updated (with summary of main changes).
  • Link to issue (:issue:number) and pull request (:pull:number) has been added.

What kind of change does this PR introduce?

Small fix upon #478. Skips even if a directory to skip is one of the entries in directory or a parent of one of the entries.
I implemented it because I misunderstood an error I was having, but still, this could be used in the specific scenario where you are running parse_directory through an incremental stack of xscen configurations. To remove en entry of the directories list of a previous configuration, you would only need to add a skip_dirs entry, and not rewrite the filtered directories.

This also adds logging calls when skipping. And a precision to the doc about the absoluteness of paths to skip.

Does this PR introduce a breaking change?

No.

Other information:

[RondeauG]

LGTM.