Wyatt,
I am in the same boat, I am not sure how you can include actionscript file into a html/js AIR application.
I have gotten to the point where extendedDesktop is supported but stuck on how to incorporate the licensing files TurboActivate.as & TurboActivateEvent.as into the html / javascript files.
I think one would need to create a swf file as a library containing the two as files and build an Actionscript to JS interface on the html page.
Would you be able to provide a sample for an Abobe Air Application built using only html and javascript. Just FYI, http://www.adobe.com/devnet/air/samples_javascript.html.
Thanks,
Vijay