I believe I understand fully the differences between Visual Studio 2005's web site model versus the web application project model that was fully delivered in VS2005 SP1 - but I have run into a confusing thing:
I have a web application project I wrote (it has a bin folder with the compiled projectname.dll and referenced .dlls too, etc.). but I just noticed that if I right-click on the project within Solution Explorer, a menu item called "Convert to Web Application" is exposed). That makes no sense to me.
I was comparing this project to a "web site" solution in VS2005 and contemplating converting it to a web application project. Strangely, the solution explorer offers nothing related to "Conversion to Web App" here like one would think is possible and/or appropriate.
I conclude there is nothing to help automate changing a "web site" construct to a proper "web application project". I assume it all has to be done by hand. Tasks such as reconstituting files in App_Code into one or more class library projects needs to be done manually.
I realize a lot has been written about the history and differences but can someone explain why the offer to "convert to web app" seems to be made in the "wrong" model - and just confirm that conversion is manual.