I have been following this post about how to build a VSIX project that will add some custom MVC project types:
http://www.asp.net/mvc/tutorials/mvc-4/custom-mvc-temp
Check out this link http://samritchie.net/2012/09/17/nuget-packages-in-vs2012-templates/ which helped me. However, I'm still running into the issue where all my references' paths are empty.
Note especially the following comment from the article linked above:
I spent a considerable period of time attempting to work out what the v2 equivalent of CustomExtension was, but to cut a long story short, you don’t need to make any changes to the .vsixmanifest — it’s enough to include all of the packages in the VSIX under a ‘Packages’ directory.