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.