As of the commit linked below, we now optionally throw out only a special div with an ID of "cappuccino-body". You should still wrap all of your index.html code inside this div, don't put content outside the special div.
The motivation here is to allow libraries which add elements to the body during the onload process to work. Specifically, the idea is that lots of flash libraries, like comet libraries, put invisible flash elements in the body for communication purposes. Those should now work thanks to this change, as long as you include the special div. All of our templates now include this div, and its trivial to upgrade the index.html files for your own older applications.
http://github.com/280north/cappuccino/commit/7ce72a31c566c164ca3ab526dc117d7254d1c6ed
Let me know if there are any problems introduced by the new system.
-Ross