utils.py: Return all directories in list_relative_paths()

Returning only empty directories leads to inconsistencies when computing
a manifest by combining results from multiple list_relative_paths()
calls as done by the compose plugin.

I.e., the same directory may be empty in one dependency and non-empty in
another dependency.  The merged file list will still contain that
directory even though it's no longer empty.

This inconsistency causes problems when calculating differences between
manifests. Returning all directories fixes these inconsistencies.

This is a change in API behavior.