Predefined type 'System.Object' is not defined or imported .net 4.6

I'm using MVC 5 and .net 4.6 to create a web API that my mobile app can connect too.

Whenever I build the project I get hundreds of errors telling me that I need to add references that are already there and that literally every type in my project 'does not exist'. Some examples of these errors: (Not including the one in the title)

What I've tried:

• Added a reference to System.Runtime via nuGet. (A recommendation from this question.)
• Removed aspnetcore50 from the frameworks in the project.json file. (Another recommendation, this question.)
• Restarting VS2015, my machine.
• Going through the nuGet package manager and upgrading every package in my project to the latest.
• Actually making sure I can see the references in the references node of the solution explorer.

UPDATE: -My project.json file looks like this. (After modifying based on Karls answer. The error list is now down to ten, however they are still the same errors as before.)

{
  "commands": {
    "web": "Microsoft.AspNet.Hosting --server Microsoft.AspNet.Server.WebListener --server.urls http://localhost:5000"
  },
  "dependencies": {
    "Microsoft.AspNet.Server.IIS": "1.0.0-beta5",
    "Microsoft.AspNet.Server.WebListener": "1.0.0-beta5",
    "Microsoft.AspNet.Diagnostics": "1.0.0-beta5",
    "Microsoft.AspNet.Mvc": "6.0.0-beta5",
    "System.Runtime": "4.0.20-beta-23019"
  },
  "exclude": [
    "wwwroot",
    "node_modules",
    "bower_components"
  ],
  "frameworks": {
    "dnx451": {
      "frameworkAssemblies": {
        "System.Data": "4.0.0.0",
        "System.Data.DataSetExtensions": "4.0.0.0",
        "System.Data.Linq": "4.0.0.0"
      }
    }
  },
  "publishExclude": [
    "node_modules",
    "bower_components",
    "**.xproj",
    "**.user",
    "**.vspscc"
  ],
  "version": "1.0.0-*",
  "webroot": "wwwroot"
}

Remove bin and obj and rebuild.

This wasted lot of my time. Close the visual studio. Delete the .vs folder and restart visual studio. Everything should work fine.

Usually this happens when you change branches or merge branches.