Web API: CMSDependencies vs NuGet

I followed the guidelines at https://docs.kentico.com/display/K82/Using+ASP.NET+Web+API+with+Kentico to build a custom Web API controller. I installed the ASP.NET Web API dependencies through NuGet in a separate class library as instructed but now I get the following error:

"Could not load file or assembly 'System.Web.Http.WebHost, Version=5.2.2.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' or one of its dependencies. The system cannot find the file specified."

And after refreshing the page:

"Original error: Could not load file or assembly 'System.Web.Http.WebHost, Version=5.2.3.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' or one of its dependencies. The system cannot find the file specified."

I suspect that there's a version conflict with the dll's that get added in the CMSApp project through the CMSDependencies folder.

• I don't get how and where these dll's are being referenced and could cause a conflict?
• Do we really need to use these versions or is there a way to use NuGet packages for all projects in the solution and delete the CMSDependencies folder from source control?

Additional questions:

• What does the AssemblyDiscoverable attribute do? Does Kentico use it to load the contained types with Reflection?
• It seems like there's some "magic" causing the CMSApp_AppCode project becoming one with the CMSApp project after building the solution. What is this magic (linked files?) ? CMSApp_AppCode doesn't seem to contain the AssemblyDiscoverable attribute. The weird thing is that when deploying, you still need to copy CMSApp_AppCode over CMSApp.