Fixed reference-prefix upgrade step:

 - Fixed typo, which wrongly updates the repository instead the dossiers.
 - Fixed CleanupReferencePrefixMapping upgrade step: Make sure annotations are persistent all the way, and add check for persistence.
 - Fixed CleanupReferencePrefixMapping upgradestep: Updates now also the mapping on the repositoryroot objects.

Fixed CleanupReferencePrefixMapping upgradestep, which adds in_persistent data to the annoations.