How can I fix assembly version conflicts with JSON.NET after updating NuGet package references in a new ASP.NET MVC 5 project?

Question

I created a new ASP.NET MVC 5 web project in VS 2013 (Update 1) then updated all NuGet packages. When I build the project, I get the following warning:

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Answer 1

I upgraded from Newtonsoft.Json 11.0.1 to 12.0.2. Opening the project file in Notepad++ I discovered both

      ..\packages\Newtonsoft.Json.12.0.2\lib\net45\Newtonsoft.Json.dll
    

and

    
      ..\packages\Newtonsoft.Json.11.0.1\lib\net45\Newtonsoft.Json.dll
    
  

I deleted the ItemGroup wrapping the reference with the hint path to version 11.0.1.

These issues can be insanely frustrating to find. What's more, developers often follow the same steps as previous project setups. The prior setups didn't encounter the issue. For whatever reason the project file occasionally is updated incorrectly.

I desperately wish Microsoft would fix these visual studio DLL hell issues from popping up. It happens far too often and causing progress to screech to a halt until it is fixed, often by trial and error.