Visual Studio does not find Newtonsoft.json dll

I have a Visual Studio Solution in which I have several Projets.

One of the projects use NewtonSoft.Json nuget, and it was once probably at 6.0.6 version, till I updated the Nugets to the latest, 12.0.1 version.

However, in runtime it was asking me for the incompatible 6.0.0.0 version, so I discovered that when I build the project it uses my windows \Users\myuser\.nuget\packages folder, in which there is Newtonsoft.json\6.0.6\ directory along with the 6.0.4 and the latest at day 12.0.1. So removed all the directories but the latest.

Now the compilation does not succeed, because

Error The package Newtonsoft.Json with version 6.0.6 could not be found in C:\Users\my-user.nuget\packages. Run a NuGet package restore to download the package. MyProject C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\MSBuild\Microsoft\NuGet\15.0\Microsoft.NuGet.targets 186

When I build with diagnostic log, I have in the output

9>PkgAutoMapper = C:\Users\my-user\.nuget\packages\automapper\3.2.1
9>PkgDefApplicationConfigFile = C:\Users\my-user\AppData\Local\Microsoft\VisualStudio\15.0_956f6176\devenv.exe.config
9>PkgjQuery = C:\Users\my-user\.nuget\packages\jquery\1.10.2
9>PkgModernizr = C:\Users\my-user\.nuget\packages\modernizr\2.6.2
9>PkgNewtonsoft_Json = C:\Users\my-user\.nuget\packages\newtonsoft.json\6.0.6
9>PkgWebGrease = C:\Users\my-user\.nuget\packages\webgrease\1.5.2

Where the hell it finds that 6.0.6 reference, I have no idea. I reinstalled multiple times the nuget Newtonsoft.json and it seems there is any old version, but the latest 12... I even searched with the Notepad in all files in the solution directory for 6.0.6 didn't find any file containing such a combination...

I spent several days and don't understand where is the problem...

My packages.config:

<?xml version="1.0" encoding="utf-8"?>
<packages>
  <package id="Antlr" version="3.5.0.2" targetFramework="net472" />
  <package id="bootstrap" version="4.3.1" targetFramework="net472" />
  <package id="CommonServiceLocator" version="2.0.4" targetFramework="net472" />
  <package id="jQuery" version="3.3.1" targetFramework="net472" />
  <package id="jQuery.Validation" version="1.17.0" targetFramework="net472" />
  <package id="Microsoft.AspNet.Mvc" version="5.2.7" targetFramework="net472" />
  <package id="Microsoft.AspNet.Razor" version="3.2.7" targetFramework="net472" />
  <package id="Microsoft.AspNet.WebPages" version="3.2.7" targetFramework="net472" />
  <package id="Microsoft.jQuery.Unobtrusive.Validation" version="3.2.11" targetFramework="net472" />
  <package id="Microsoft.Web.Infrastructure" version="1.0.0.0" targetFramework="net45" />
  <package id="Modernizr" version="2.8.3" targetFramework="net472" />
  <package id="Newtonsoft.Json" version="12.0.1" targetFramework="net472" />
  <package id="popper.js" version="1.14.3" targetFramework="net472" />
  <package id="System.Runtime.CompilerServices.Unsafe" version="4.5.2" targetFramework="net472" />
  <package id="Unity" version="5.10.3" targetFramework="net472" />
  <package id="Unity.Abstractions" version="4.1.3" targetFramework="net472" />
  <package id="Unity.Container" version="5.10.3" targetFramework="net472" />
  <package id="Unity.Mvc" version="5.10.1" targetFramework="net472" />
  <package id="WebActivatorEx" version="2.2.0" targetFramework="net472" />
</packages>

From my.csproj file:

<Reference Include="Newtonsoft.Json, Version=12.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed, processorArchitecture=MSIL">
  <HintPath>..\..\MyFront\packages\Newtonsoft.Json.12.0.1\lib\net45\Newtonsoft.Json.dll</HintPath>
  <Private>True</Private>
</Reference>

Project's WebConfig:

  <dependentAssembly>
    <assemblyIdentity name="Newtonsoft.Json" publicKeyToken="30ad4fe6b2a6aeed" culture="neutral" />
    <bindingRedirect oldVersion="0.0.0.0-12.0.0.0" newVersion="12.0.0.0" />
  </dependentAssembly>

New Solution and new project

I tried to create a new project as "Empty Web Project" when it tries to add it so the solution an error message appears:

== Microsoft Visual Studio ==
Could not load file or assembly 'Newtonsoft.Json, Version=6.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)

I repaired Visual Studio... (I start to hate Visual Studio), spent half a day to repair it, but any success... I now try to recreate a new solution with new projects from the existing code