Asp.net5 / dnx Cannot resolve the link when publishing, but can it be debugged?

Question

So this seems a little strange, I have a dnx command line application which is the only solution referencing 4 other .net 4.5 classic projects (aka.csproj). I can execute the code and debug it without any problems. However, I can not start it after its publication.

The application starts up and shows some output from Console.Write, and then tries to run some code that db requests using Entity Framework v6.1.3.

The error I get is "Could not load file or assembly" EntityFramework, Version = 6.0.0.0 "

which seems odd, since all the links relate to 6.1.3, and it works fine with VisualStudio but doesn't use any commands when publishing.

I am using dnx 1.0.0 rc1 update1

- update Just to make sure something is wrong with the solution. I blew it and recreated it in the source files needed ... Still the same problem. I am adding project.json

 {
  "version": "1.0.0-*",
  "description": "What.BotApprover Console Application",
  "authors": [ "bferr" ],
  "tags": [ "" ],
  "projectUrl": "",
  "licenseUrl": "",

  "compilationOptions": {
    "emitEntryPoint": true
  },

    "dependencies": {
        "Microsoft.Extensions.Configuration": "1.0.0-rc1-final",
        "Microsoft.Extensions.Configuration.CommandLine": "1.0.0-rc1-final",
        "Microsoft.Extensions.Configuration.Json": "1.0.0-rc1-final"
    },

    "commands": {
        "What.BotApprover": "What.BotApprover",
        "run": "What.BotApprover --appconfig C:\\dev\\What.com\\Trunk\\AutoSpark\\src\\AutoSpark\\configs\\app.config --test true",
        "AutoSpark.BotApprover": "What.BotApprover"
    },

  "frameworks": {
    "dnx451": {
        "dependencies": {
            "What.Common": "1.0.0-*",
            "What.Common.Utilities": "1.0.0-*",
            "What.Data": "1.0.0-*",
            "What.EventCache": "1.0.0-*"
        }
    }
  }
}