Just to help out anyone who has landed on this page after updating VS2015 to update 2 and trying to manage packages on a website, receiving the "NuGet configuration file is invalid" error, this is a known and acknowledged issue:
I got mine working again by installing package manager 3.4.4 (beta) from http://dist.nuget.org/index.html
They do also state update 3 for Visual Studio will also contain a fix