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
Same comment for all the other app.config and redirects below. My guess is they're not needed. In fact, appconfig is likely not used at all in the context of running tests, so if tests pass, it's a good sign they're not needed.