MVC6 FileNotFoundException: System.Data.SqlClient

It is probably due to version conflicts in assemblies, Microsoft have developed a tool named Microsoft ASP.NET and Web Tools 2015 (Beta6) – Visual Studio 2015 to resolve the best suited versions for current assemblies. https://www.microsoft.com/en-us/download/details.aspx?id=48222

Better use this and start your project. But is you still wants to stick with the project your project.json should look something like this.

"dependencies": {
    "System.Collections": "4.0.10-beta-23109",
    "System.Linq": "4.0.0-beta-23109",
    "System.Threading": "4.0.10-beta-23109",
    "System.Runtime": "4.0.10-beta-23109",
    "Microsoft.CSharp": "4.0.0-beta-23109"
  },

  "frameworks": {
    "dnx451": {
      "dependencies": {
      },
      "frameworkAssemblies": {
        "System.Data": "4.0.0.0"
      }
    }
  }