I am first and foremost, a ColdFusion developer. And I’m a little idiocyncratic as to how I organize my projects in directories and files. My “project root” is not web-accessible, but usually contains ALL the project assets, including CFCs, CFMs, etc.
I got really annoyed that Flex Builder put everything in my workspace when creating a new Flex Project. It was not immediately intuitive how to move the main application .mxml source file outside of the workspace. And I wasn’t about to point my project path to my webroot because it would put all the Eclipse and Flex Builder property files there (which would clutter up the Subversion repository for the project).
So after about two days of futzing and conferring with more experienced Flex developers, I figured out exactly how to tweak all the poorly-documented settings in the Flex project Properties to accommodate me. Now I keep the Flex project in my workspace, but all the source files and compiled swfs end up in my webroot’s project directory, and thusly in Subversion via a single click.
I mostly documented this for myself for future reference, but hope you find it helpful. The screencast is about 13 minutes long (made with Camtasia Studio) and is a 14MB file.