since swc files usually go to the lib folder, I've been using "fla" as the fla files folder for quite some time now, and everything looks neater... for me

The only drawback, I need to manually edit every FLA file to add the lib folder to the classpath, OR use a common folder (swf) for every fla file except main an preloader, and add the ../../lib to the lib classpath in the template fla folder before scaffolding. I tried to hack the scaffold.jsfl file a few days ago with no success, I'll probably dig on it later