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
Didn't realize we used that SDK. Anyway, if that's what it takes to make things happy, it's not a huge deal.