These are just scattered thoughts about the organization for projects that work primarily with the Flash IDE.
First, I highly recommend using a control source like Subversion, CVS, or Git.
The structure of the file system's folder structure is subjective, but usually I have a βsrcβ folder for all FLA and AS-class source files and a βexpandβ or βbinβ folder for compiled files. The src folder will contain class class files, and class packages are organized in the reverse domain style (for example, com.codehinting.projectname.context). Change the publishing path of your FLA to publish it to the deployment folder by backing up the "../" path segment with as many levels as you need to track from nesting in the src folder.
In addition, I usually place third-party libraries (which are pretty well baked) in a separate place, and then modify the global class path in the Flash IDE to point to this location.
Two extremely convenient plugins for the Flash IDE are Create Basic Layers and Library Generator, which quickly create your skeleton layer and library folder structure - saving time and manually creating layers and folders.
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