I just posted a new FlexJSOverlay.zip at FlexJSOverlay.zip at [1]. It contains most recent dependency management and strict output corrections from Erik, and also contains better FB integration. You will need to remove your old FlexJS launch configurations and import new ones to get the benefit of this change. The new launch configs pass a -fb flag to Falcon which then reads the FB project files to determine the main compilation unit and other options. Not all MXMLC options are currently supported, so feel free to add new ones or file bugs about other missing ones. The key benefit of this change is that you no longer have to click on the main mxml file before running the launch configurations. Falcon can now figure it out based on what project you've selected in the package explorer and/or what file you are editing.
As always, feedback and contributions are welcome. -Alex [1] http://people.apache.org/~aharui/FlexJS/FlexJSOverlay.zip