Updating Newtonsoft.Json to 6.0.6

We use Json.NET to parse `project.json` for ASP.NET 5 projects. They use Json.NET 6 and the main issue is that they include single-line comments in the json files which is not supported in 5.x
I tried removing them, but got many build errors, that I thought it's needed. Apparently it's a [known Azure SDK v2.3 bug](https://connect.microsoft.com/VisualStudio/feedback/details/850425/windows-azure-vs-tools-breaking-msbuild-for-web-projects) that it changes the default targets to include Newtonsoft 4.5.0.0. I will uninstall that SDK and update the pull request.