[WFLY-122] : Clean unreferenced items from the content repository

Contents in content repositories are now cleaned. We are looking for all referenced contents in the model :
 * deployments
 * overlays
 * rollout-plans
All contents that are not referenced will be removed.

Jira : https://issues.jboss.org/browse/WFLY-122
Javadoc is out of date. Please check the other methods too.