Could not load file or assembly 'Newtonsoft.Json, Version=6.0.0.0

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)

Yes, I use the 12.0.0.1

Each time I have this kind of issue I know I will have a bad moment. Once for all I would like to understand what is happening here.

I have 4 projects in my solution. Same settings

Same reference version 12.0.0.0. I checked:

csproj file seems ok for all of them too:

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

I cleaned my project with Visual Studio but also with Tortoise Git to delete all files not managed by my repository. this include the Nuget dll. So I build with fresh correct version of dll.

I can run my project locally but when I deploy on my staging server on IIS I get the error. It seems I have a wrong dll on my server, possible? Why version 6.0.0.0? Nothing is related to this version in all my code.

--------- EDIT

Here is my web.config. I removed the connectionStrings and appSettings parts.

  <configSections>
    <section name="entityFramework" type="System.Data.Entity.Internal.ConfigFile.EntityFrameworkSection, EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" requirePermission="false"/>
    <!-- For more information on Entity Framework configuration, visit http://go.microsoft.com/fwlink/?LinkID=237468 -->
  </configSections>
<system.web>
    <compilation debug="true" targetFramework="4.7.2"/>
    <httpRuntime targetFramework="4.6.1"/>
    <httpModules>
      <add name="TelemetryCorrelationHttpModule" type="Microsoft.AspNet.TelemetryCorrelation.TelemetryCorrelationHttpModule, Microsoft.AspNet.TelemetryCorrelation"/>
      <add name="ApplicationInsightsWebTracking" type="Microsoft.ApplicationInsights.Web.ApplicationInsightsHttpModule, Microsoft.AI.Web"/>
    </httpModules>
  </system.web>
  <system.webServer>
    <validation validateIntegratedModeConfiguration="false"/>
    <modules>
      <remove name="TelemetryCorrelationHttpModule"/>
      <add name="TelemetryCorrelationHttpModule" type="Microsoft.AspNet.TelemetryCorrelation.TelemetryCorrelationHttpModule, Microsoft.AspNet.TelemetryCorrelation" preCondition="managedHandler"/>
      <remove name="ApplicationInsightsWebTracking"/>
      <add name="ApplicationInsightsWebTracking" type="Microsoft.ApplicationInsights.Web.ApplicationInsightsHttpModule, Microsoft.AI.Web" preCondition="managedHandler"/>
    </modules>
    <handlers>
      <remove name="ExtensionlessUrlHandler-Integrated-4.0"/>
      <remove name="OPTIONSVerbHandler"/>
      <remove name="TRACEVerbHandler"/>
      <add name="ExtensionlessUrlHandler-Integrated-4.0" path="*." verb="*" type="System.Web.Handlers.TransferRequestHandler" preCondition="integratedMode,runtimeVersionv4.0"/>
    </handlers>
  </system.webServer>
  <runtime>
    <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
      <dependentAssembly>
        <assemblyIdentity name="Newtonsoft.Json" culture="neutral" publicKeyToken="30ad4fe6b2a6aeed"/>
        <bindingRedirect oldVersion="0.0.0.0-12.0.0.0" newVersion="12.0.0.0"/>
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="System.Web.Optimization" publicKeyToken="31bf3856ad364e35"/>
        <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="1.1.0.0"/>
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="WebGrease" publicKeyToken="31bf3856ad364e35"/>
        <bindingRedirect oldVersion="0.0.0.0-1.6.5135.21930" newVersion="1.6.5135.21930"/>
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="System.Web.Helpers" publicKeyToken="31bf3856ad364e35"/>
        <bindingRedirect oldVersion="1.0.0.0-3.0.0.0" newVersion="3.0.0.0"/>
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="System.Web.WebPages" publicKeyToken="31bf3856ad364e35"/>
        <bindingRedirect oldVersion="1.0.0.0-3.0.0.0" newVersion="3.0.0.0"/>
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="System.Web.Mvc" publicKeyToken="31bf3856ad364e35"/>
        <bindingRedirect oldVersion="1.0.0.0-5.2.6.0" newVersion="5.2.6.0"/>
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="Antlr3.Runtime" publicKeyToken="eb42632606e9261f" culture="neutral"/>
        <bindingRedirect oldVersion="0.0.0.0-3.5.0.2" newVersion="3.5.0.2"/>
      </dependentAssembly>
      <dependentAssembly>
        <assemblyIdentity name="System.Diagnostics.DiagnosticSource" publicKeyToken="cc7b13ffcd2ddd51" culture="neutral"/>
        <bindingRedirect oldVersion="0.0.0.0-4.0.3.1" newVersion="4.0.3.1"/>
      </dependentAssembly>
    </assemblyBinding>
  </runtime>
  <entityFramework>
    <defaultConnectionFactory type="System.Data.Entity.Infrastructure.SqlConnectionFactory, EntityFramework"/>
    <providers>
      <provider invariantName="System.Data.SqlClient" type="System.Data.Entity.SqlServer.SqlProviderServices, EntityFramework.SqlServer"/>
    </providers>
  </entityFramework>
  <system.codedom>
    <compilers>
      <compiler language="c#;cs;csharp" extension=".cs" type="Microsoft.CodeDom.Providers.DotNetCompilerPlatform.CSharpCodeProvider, Microsoft.CodeDom.Providers.DotNetCompilerPlatform, Version=2.0.1.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" warningLevel="4" compilerOptions="/langversion:default /nowarn:1659;1699;1701"/>
      <compiler language="vb;vbs;visualbasic;vbscript" extension=".vb" type="Microsoft.CodeDom.Providers.DotNetCompilerPlatform.VBCodeProvider, Microsoft.CodeDom.Providers.DotNetCompilerPlatform, Version=2.0.1.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" warningLevel="4" compilerOptions="/langversion:default /nowarn:41008 /define:_MYTYPE=\&quot;Web\&quot; /optionInfer+"/>
    </compilers>
  </system.codedom>

--------- EDIT 2

Let me also add you the first line of the error stacktrace because I have 2 reference errors in fact: missing of version 6.0.0.0 then the same for version 11.0.0.0. What?

[FileLoadException: 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)]

[FileLoadException: Could not load file or assembly 'Newtonsoft.Json, Version=11.0.0.0, 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)]
   System.Net.Http.Formatting.BaseJsonMediaTypeFormatter..ctor() +0
   System.Net.Http.Formatting.JsonMediaTypeFormatter..ctor() +73
   System.Net.Http.Formatting.MediaTypeFormatterCollection.CreateDefaultFormatters() +55
   System.Web.Http.HttpConfiguration.DefaultFormatters(HttpConfiguration config) +34
   System.Web.Http.HttpConfiguration..ctor(HttpRouteCollection routes) +388
   System.Web.Http.<>c.<CreateConfiguration>b__11_0() +94
   System.Lazy`1.CreateValue() +243
   System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw() +32
   System.Lazy`1.get_Value() +14280552
   SerialGenerator.Areas.HelpPage.HelpPageAreaRegistration.RegisterArea(AreaRegistrationContext context) in D:\a\1\s\SerialGenerator\Areas\HelpPage\HelpPageAreaRegistration.cs:18
   System.Web.Mvc.AreaRegistration.RegisterAllAreas(RouteCollection routes, IBuildManager buildManager, Object state) +231
   SerialGenerator.WebApiApplication.Application_Start() in D:\a\1\s\SerialGenerator\Global.asax.cs:17