I don't quite understand your question. Could you phrase it another way?
Ok. Ask again.
produces the output file in AS3 or Flash?
The native format of Catalyst is FXP, which is a zipped up Flex Project. A Flex Project contains MXML and AS3 code, as well as image assets. When you run or publish the project, it is compiled to SWF. The SWF file is what you deploy on your web server.