First, It is not just duplicate. None of answers from following questions are working for me.
http://goo.gl/tS40cn
http://goo.gl/pH6v2T
I\'ve just updated al
Run Update-Package Newtonsoft.Json -Reinstall
It should remove the reference to your 4.5 version, and reinstall the newer version referenced in your package.config. It will also update the binding redirect, which should then be as follows:
Since you said in your question that you already tried this, you might want to first try removing the existing reference manually. You might also want to make sure the files aren't read-only on disk, or otherwise locked by source control.