Yes, Oni Apollo is open-source, and you've got the right repository. The assembled library, oni-apollo.js, is composed of a whole bunch of different bits and pieces and tools which we'll all be publishing on github eventually. It will take a bit of time, so please bear with us.
The source code for the built-in modules is already there, see http://github.com/onilabs/apollo/tree/master/src/modules/ .
