Background
I started to build a multi-project template and soon found little consistent information online across both Developer Network documentation and the wider community. It seems between VS 2010, 2012 and 2013 there has been quite a number of changes for building a multi-project template.
My initial problems resolving the $safeprojectname$ in the using statements found me here where I soon realized didn't work and was probably more related to VS2010. However, I found out that VS2013 had been changed to incorporate $ext_safeprojectname$ to resolve this exact problem without the need for a wizard.
Current issue
My VSIX installs, my solution constructs with the name you have chosen. You hit build and it goes out to get missing packages, it places them in a packages folder, but the reference paths are missing. I looked to this documentation at nuget.org which appears to be for VS2012 and now out of date. The packages are listed in the vstemplate, the repository is set to the VSIX product ID, but the CustomExtension doesn't seem to work wherever I put it and it completely ignores the nupkg files I added to the VSIX. The vsixmanifest doesn't even support the CustomExtension as an asset anymore. I also tried it in the vstemplate and it has no effect.
The only thing that I have found that works is to create the solution, enable package restore on the solution, go to the command line and put:
..\.nuget\nuget.exe install -o packages "example\packages.config"