[WFCORE-213] :  Clean unreferenced items from the content repository

Now we are using ContentReference to track contents in the content repository.
Now we are tracking references to overlays.
Trying to use server group definition for domain mode.
Simplifying ContentReference
WFCORE-211: Fixing overzealous cleaning of HC content.
[WFCORE-213] :  [WFCORE-178] :  ContentRepositoryImpl should not call File.deleteOnExit when deleting content.

Using the new Path API instead of File.
Cleaning empty old directories.