Here is an idea:
ShinyDeploy should consist of submodules to the original repos in which we are developing apps. Each submodule could link, e.g., to a deploy branch, so that development could still happen in master.
Here's an example:
Legend and ShinyDeploy link via submodule to LegendBasicViewer. The Legend link is for all branches and the ShinyDeploy link is for the deploy branch.
Other ideas?