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

We are using ContentReference to track contents in the content repository.
Se 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-178: ContentRepositoryImpl should not call File.deleteOnExit

Jira: https://issues.jboss.org/browse/WFCORE-213
and https://issues.jboss.org/browse/WFCORE-211
and https://issues.jboss.org/browse/WFCORE-178
Please pass 'false' to readResourceFromRoot to avoid unneeded cloning of child resources.