Differences between Web Site Project and Web Application Project

I have been working on both kinds of web projects since I started developing on ASP.Net. After manually migrating a Web Site into a Web Application Project, I now understand the differences:

Topic	Web Site	Web Application
Project Files	All files in and below the project directory	All files added to the .csproj project file
MasterPage Reference	Add “Web Form” and check “Select master page”	Add “Web Content Form”
Assembly Namespace	Global namespace	Namespace as defined in project
Generated assemblies	Code in the App_Code directory compiles into a single assembly. Code from code-behind files compile into various assemblies named App_Web_*.dll. Assemblies can be merged using aspnet_merge.	Compiles into single assembly
Code Restrictions	Since code-behind is generated into randomly named assemblies, code in one page or control almost certainly cannot reference any other page or control. (Work-around: extract to base class or interface inside App_Code)	Code under the App_Code directory is ignored. (Solution: rename App_Code directory)
Complete build	Build from command line using aspnet_compiler	Add aspnet_compiler as Post-build Event
Publish	Publish from command line using aspnet_compiler and aspnet_merge	Publish from command line using msbuild /property:OutDir=(path)
Published files	Contents of aspx and ashx files is replaced by the text “This is a marker file generated by the precompilation tool, and should not be deleted!”. The Bin directory contains a (filename).(8hexdigits).compiled file for each compiled markup file listing the original dependencies.	Original aspx, ascx, master files remain. ashx files refer to their implementation class.