You can do this in two ways. Electric Imp provides builder, which is a command line tool that can do this kind of thing. It’s cross-platform.
Separately, if you’re a Mac user, there is also Squinter, which is a GUI-based tool for managing Squirrel projects across multiple local files (which can be in a sync’d folder or a local GitHub repo clone). It also provides device management and logging.
Squinter 1.0 works with IDE-style models, but these will shortly be replaced by impCentral’s Products and Device Groups. You need Squinter 2.0 to work with these.