While CloudMan is still very much a part of the Galaxy project, and is also used as the infrastructure manager in the GVL project, it has been going through a lot of change lately because it was rewritten from the ground-up to support Kubernetes. Therefore, we are no longer developing the old version of CloudMan, and the focus is on v2. You can launch alpha versions of this CloudMan version by selecting CloudMan 2 or GVL 5 alpha, which are more or less the same thing at present.
CloudMan will provision VMs on the target cloud, setup a Kubernetes cluster on it, and deploy a Kubernetes Helm Chart for Galaxy (https://github.com/galaxyproject/galaxy-helm), and therefore, customising Galaxy is a matter of customising the Helm chart.
Alternatively, you can also deploy your Galaxy Helm chart directly if you already have an existing k8s cluster and do not need CloudMan to manage it. The Galaxy Helm chart has already gone through a few iterations and we consider the interface to be fairly stable.
Yet a third option would be to use the docker galaxy stable container (https://github.com/bgruening/docker-galaxy-stable/tree/master/galaxy) depending on the kind of modifications you need.
Let us know if you have any follow up questions.