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
NuGet package restore does not modify the project files. It just downloads and extracts the NuGet packages to the packages directory.
If you are trying to edit the packages.config file and then have the project's updated you would have to use the Package Manager Console and run:
Update-Package -reinstall
Which will uninstall and install the packages again and update the project's references.