I have a current website project that I need to migrate to Windows Azure. Back in 2009 we had to convert the website project to a web application project. Is that still the case today?
Your life will probably be a lot easier if you use web application projects, but you can use website projects. At the very least, you can use cspack from the command line and point it at any directory. You can also use the physicalDirectory attribute in ServiceDefinition.csdef to point to an arbitrary directory. That directory can be your website project.
I'm not sure if there are better ways from within Visual Studio to use a website project as a web role.