I am trying to adjust my Flash development workflow so that I am using Flash Builder for all of my coding and multiple FLA files for the user interfaces. I will be creating
You can build an AIR application from a pure ActionScript project. Apparently it's not as obvious as it should be, but here's one way of doing it:
http://ted.onflash.org/2010/03/air-apps-using-actionscript-only.php
Also the very latest version of AIR (currently in RC stage, so stable enough to use, final version will be released soon) can package the app into an EXE so you don't need to install the AIR framework separately.
AIR packages can also be compiled from the commandline, so should be easy to integrate into a separate build process if you don't want to do it from the Flash Builder GUI.