I recently migrated all my Visual Studio 2013 projects to Visual Studio 2015 and followed the steps documented in this article by Nuget to make sure that automatic package resto
Something I just noticed, and I'm not sure if this will help you or anyone else reading this, but this issue literally wracked my brain. The problem was that I was installing packages that I had created myself using NuGet Package Explorer on Windows.
It turned out that, I believe after updating NuGet Package Explorer, it was no longer putting DLLs that I included into the lib
folder. Once I started manually adding the lib
folder back into the package within Package Explorer, and then uploading to NuGet and reinstalling in the consuming project, that the reference would once again start to appear.
I'm not sure what caused this behavior - it could have been my own fault, but I literally just now figured this out - and consequently have to go back and re-do a whole bunch of NuGet package goodness that I've done over the past month. OUCH.
Hope this saves someone at least an ounce of pain.