The Document Generation Services Management Tool library deploy no longer updates content references with the Management deploy; you will now need to run the command line to update content references prior to create the library .ZIP file.
Additionally, a -nocopy switch has been enabled for the content deployment. This automatically builds the content by placing the documents at a specific organization level without copying ancestor-level documents. The Document Generation Management Tool has been udpated with a new Expere Admin .DLL that implements the -nocopy switch.
Consult the Document Generation Services Management Tool User Guide for more information on running the command to update content references for creation of the library .ZIP file.