It looks like several things changed with some latest changes (October 7th) in the develop branch. I created two examples of installing modules. One that copies files to app/code and another that registers the module where it resides in the vendor directory.

Copy Strategy: https://github.com/mttjohnson/magento2-sample-module-minimal-copy  
Registration Strategy: https://github.com/mttjohnson/magento2-sample-module-minimal-register

For development purposes I think utilizing the registration strategy is more useful because the files that are being run by Magento can be directly modified, tested and then committed back to the module repo.