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first, those folders are necessary in deployment - You need only the contents of the bin folder for deployment, not the sources. Since you're compiling the application locally in FB2 it places all of the supporting and necessary files into one location namely the "bin" folder. You'd deploy the "bin" folder's contents to the FDS server, perhaps another FDS server that is not your "development" server -- like a production server. The data and configuration information that your app needs for FDS services are stored in the WEB-INF and META-INF folders so these need to travel with the final product. On the production server you'd just cop the "bin" folder and it's contents to the /servers/default folder - where you could then rename your bin folder to "MyDS"
Bill, thank you for the clarification. I understand now that during deployment of the app to the "Production FDS" I will need to copy a "bin" folder.
I still need to better understand what is going on during the development cycle. My development environment is configured on a single machine with FB2 project created under the JRun integrated server "default" server. Now, if I need to modify, for example, WEB-INF\services-config.xml file should I modify it in the WEB-INF folder that sits OUTSIDE "bin" folder? If the answer is "yes", how and when two service-config.xml files are synchronized? Is it done by Flex Builder every time I make a change or should I track the changes myself and manually synchronize them?