The Console now uses the functionality provided by the repository managers. Also, a bug in the repository managers was fixed that prevented directory removal for uninitialized repositories.
One can run the 'create' command again to reconfigure a repository. After specifying the (new) configuration parameters, the console will warn you that you're about to overwrite an existing configuration. Simply enter 'yes' to continue doing so.
Before implementing this behavior, I would ask that you provide an easy alternative for changing an existing repository configuration without deleting data (e.g. to add an index) - currently the only way that works for me is to drop and re-create the repository, which relies on keeping the data around. Every time I try to directly manipulate the system repository I end up breaking something (the web interface does not reliably allow you to update BNodes) - so if drop is going to delete data, it should be supplemented by a "reconfigure" command to allow configuration changes to existing repositories.