This FlashDevelop project allows you to build PBE from the src directory, but
you'll still need to set the path to your Flex SDK. If you've used FlashDevelop
before, this is probably already done. See PBE Lesson 1 for more information.

If you'd like to build a SWC instead of a SWF you can do so with the ANT build
script in the build directory, or by using the ExportSWC plugin for FlashDevelop.
The plugin is located at: 
http://www.flashdevelop.org/community/viewtopic.php?t=2987&start=0