RE: " I add or remove partitions or make other changes to the cluster " I think these scripts are designed to make it really easy to set up and tear down the cluster but it's not so easy to modify an existing cluster. So the operational tasks are left as an exercise to the reader. Check out the archives of this mailing list for tips for how to do things like change the number of compute nodes or change the specs of the compute nodes or change the shared filesystem mounts on the compute nodes or add a piece of software to the node image.
It's definitely designed to just pre-define everything and deploy and use and tear down. It may be quicker and easier to tear down the existing cluster and make a new one with the change you want. You'll have to play with all that yourself and try to fit it for your use case.
For example, in my case I found it easy to launch a cluster per-user-project with the instance types based on the job script specs the user comes to me with. Completely separate cluster for each user and dataset.