Uploading your web application from Github
At the moment, when deploying to Cloud CMS the pull is from the master branch.
A feature request is queued to add the ability to specify branches. This would allow you to set up multiple deployments and different Git branches per deployment. It would essentially merit having an extra text field where you can supply the branch name. If not provided, the master branch would be assumed as it is right now.
Note that this is only necessary if you're deploying to our app server either for hosting purposes or for CDN/asset retrieval and caching. If you're running your app standalone (such as if you're hosting it yourself), then Git branches and your dev process are completely outside of Cloud CMS for purposes of application deployment.