GERONIMO-5988 duplicates this issue.
A new instance requires var, etc, and repository else it won't start up.
The documented method is a straight copy of these directories to the instance directory.
A problem with this method is if the directories being copied have already been modified from a separate run-time execution. deploy:new-instance would only copy the directories instead of generating new "default" directories. So after a person make this call, then they have to go and make modifications to these directories on the local disk to set up the instance.
If we are going to have a gogo/karaf command to do this for us, what we really need is to have the var, etc, and repository directories generated new each time deploy:new-instance is called. And still then, we need a way to configure the new instance from gogo/karaf commands as well.
Otherwise, we might as well abandon this procedure and use a different procedure that allows us to deploy an archive that contains an admin-user-modified var/etc/repository bundle.
Or I guess, deploy:new-instance could allow (optionally) a new-instance-archive to be passed in as an argument.