Here the story, at first I created new empty solution with name TestSolution. Next I added new project with name TestProject and add EntityFramework 6.1.3 reference via NuGet Package Manager. After that NuGet Package Manager create folder packages and add Reference
<Reference Include="EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089, processorArchitecture=MSIL">
<HintPath>..\packages\EntityFramework.6.1.3\lib\net45\EntityFramework.dll</HintPath>
<Private>True</Private>
</Reference>
After a while I decided to create subfolder with name Subfolder and move TestProject there.
I excepted what new Reference will looks like
<Reference Include="EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089, processorArchitecture=MSIL">
<HintPath>..\..\packages\EntityFramework.6.1.3\lib\net45\EntityFramework.dll</HintPath>
<Private>True</Private>
</Reference>
How can I move project and update references without manual update project files?