The message Please shut down your instance, run updateDataItemNodeDefinition.py script in data module bundle to update data node type definitions and start instance again. is little bit confusing because it looks like there is no other way how to proceed than running python script. But actually it is not true, users can do update manually.
We should update this message and tell users they can either run python script or update custom_nodetypes.xml manually (it would be to give them some link to release notes in the message itself).