The easiest way to work with this would be to clone the repo somewhere on disk and then place an alias (mac OSX) of the desired external modules into the JUCE modules folder. Unfortunately, the introjucer fails to recognise the aliased modules folders. Would it be possible to add this feature?
Alternatively you could use a symbolic link which are automatically resolved. This is how I use external modules.
From the terminal:ln -s <source> <target>.