I needed to create a WebApplication, but deploy it as a standard ASP.NET website using "CodeFile" attributes.
This was basically to update a page in the standard ADFS login site.
<files>
<file src="**" exclude="**\*.dll;**\*.designer.cs;**\*.csproj;**\*.pdb;**\*.user;**\*.vspscc;bin\*.cs;bin\*.aspx;bin\*.config;bin\*.asax;bin\*.pubxml" />
</files>