Hi David,
I'm afraid some of that is embedded in CloudMan's code. Given you're restarting your cluster, you can unpack cm.tar.gz from your cluster's bucket (you can find this on CloudMan's Admin page) and edit
cm/util/galaxy_conf.py to change the value for desired variables (under
populate_galaxy_paths method). Once you're done, just create the tarball of the source again and upload it back to your cluster's bucket.
Let us know if you that doesn’t work for you. We're working on a better solution for this.