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
I happened to come across the same problem. i tried all the possible solution but found the solution - just open the .proj file in an text editor and check the package Version and the HintPath in the Reference tag. Sometime there is an mismatch correct it then Visual studio will recognize. I hope everyone can save lot of time. Here is an sample to refer
<Reference Include="nunit.framework, Version=3.4.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb">
<HintPath>..\packages\NUnit.3.4.1\lib\net45\nunit.framework.dll</HintPath>
</Reference>