ASP Web site to Web Application problems
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I am attempting to convert a very large asp.net web site project into a web application project. The main reason is we want to refactor the code to enable unit testing.
The Web site is written in .net 4.0. 

I first attempted this using this walkthrough:
http://msdn.microsoft.com/en-us/library/aa983476.aspx

After this conversion there was 1500 errors when trying to build! Not Good!
I did note however that during the conversion when I copied across the web site files and folders and performed the convert to web application my App_Code folder was not renamed as the guide said it would be, it remained App_Code.

I went hunting for other methods and tried this guide to converting:
http://blogs.msdn.com/b/webdev/archive/2009/10/29/converting-a-web-site-project-to-a-web-application-project.aspx
 which is very similar but with the slight difference of copying the App_Code folder first and converting that, then do the same with the remaining files. Sadly this still had the same effect, the App_Code folder was not renamed.

From looking at the hundreds of errors, the majority seem to be where any code (Code behind files) references code which was stored in the web sites App_code folder. Even code in the App_Code which has namespaces in place are giving errors.

Example: The type or namespace name 'SampleNamespace' could not be found (are you missing a using directive or an assembly reference?)

I may be missing something simple, but has anyone had similar issues when performing this type of conversion? Or know where I am going wrong?

Any help is much appreciated.
Thanks 
Ryan