VS2015 nuget package manager not finding packages

This is a known issue with nuget version 3.4, which is included with Visual Studio 2015 Update 2:

The NuGet.config file in your %AppData%\NuGet\ folder has accidentally been emptied. To fix this: Close Visual Studio 2015, delete the NuGet.config file in the %AppData%\NuGet\ folder and restart Visual Studio. A new NuGet.Config file will be generated and you will be able to proceed.