Package cleanups

[arteymix]

• move ubic.gemma.persistence under ubic.gemma.core.persistence
• move ubic.gemma.persistence.util under ubic.gemma.core.util (if not relevant to persistence API)
• move VOs into gemma-web (or wherever they are being used) to keep ubic.gemma.model minimal (I really like this package since it makes a clear distinction between our models the business logic of gemma-core)
• move ubic.gemma.web.services.rest under gemma.rest (see Let the RESTful API have its own package under ubic.gemma #218)
• move ubic.gemma.core.apps to ubic.gemma.apps

Also, because of ACLs, we cannot relocate ubic.gemma.model.