When I create default web project in Visual Studio 2015 (Update 3) with installed .NET Core 1.0 SDK and Tooling (preview 2) and restart the Visual Studio after reverting loc
In my case the problem was that one of the class library projects in a solution was referencing an AspNetCore.Identity library by the absolute path when I pulled sources from the source control. Because of that - wrong paths were generated in project.fragment.lock.json file and solution couldn not build.
Fixing that absolute path reference in .csproj file made it work.