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AIR applications can't run inside the browser. For that you need a Flex application.
Except for the AIR specific stuff (like native windows, file, system tray, etc), other stuff will easily compile into a flex application without change. Modularize your code so that there's a common set of code that both your flex and AIR application uses and then there's flex / air specific stuff.
OK. That helps. I realised reading the File Class documentation that that class was not going to work in a browser anyway. Thats fair. My next query taking this forward is: