You can use mxmlc to compile your app into a SWF file. Here is how it generates my release build:
mxmlc code/Main.as -o bin/Qyx2.swf -define=CONFIG::Android,false -define=CONFIG::Debug,false
The most important parts are the first argument which tells it what to compile and the second
-o which tells it where to put the output.
It only needs one file as input as that references all the other classes inside packages which means it can find them. Any art or other assets are included using
adt can then be used to turn the SWF into an APK, incorporating the manifest and other assets.