The fact that FlashBuilder creates an entire project doesn't really matter. I usually create an Actionscript project and use the main class as the entry point to the set of classes I want to create.
In the project properties, I add a folder to my source path, and inside this folder I create packages that I want to work with
source directory
com/
mydomain/
mainpackage /
Thus, my classes are completely independent of my project.
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