Rework from_disk.Directory.from_disk() implementation
It used to traverse all the directory and filter elements of said tree only afterwards; this version should be a bit smarter and not go too far deep in directories that should be ignored.
We cannot just use the subtree eviction mechanism of 'os.walk(topdown=True)' because the filtering callback takes some context of the subdirectory content (typically to be able to evict empty directories).
This version of the code is a bit more complex but should do the trick.
One questionable point is about the behavior of the ignore_directories_patterns() filter (see the added test the revision 'Rework from_disk.Directory.from_disk() implementation' of this MR for more details)
Also comes with a small refactoring introducing a helper mk_tree() function to make tests involving a directory tree structure a bit easier to read.