I'm in a group which is starting to develop using InterSystems Ensemble (an integration framework built on top of InterSystems Caché).
InterSystems has not made the Ensemble Management Portal source-control-aware and this seems a source of problems for development team we would like to address.
I would like to know which version control system are you using for Ensemble/Caché and how are you structuring your development process around it.
If you are not afraid by development work, you can make some development to hook studio to your current source control tool. There are hooks in place in Cache that allows you to detect modifications on files and to interact with your source control tool.
Here a link to a pdf the describes the basis : Using the Studio Source Control Hooks
Of course with this solution you will have to do a lot of work on your side.