The solution to that I've been using is to have a "skeletal" mx:application file in the root directory. that skeletal file does something like this:
<mx:Application ...
xmlns:view="com.mycompany.yadayada.*"
<view:MyAppMain
....
/>
</mx:Application>
the MyAppMain.mxml is a component living in
the "com.mycompany.yadayada" path that contains the real application.
Since its a component it can be bundled easily with other "main"
screens if I wanted to do so.
