Two reasons this would be useful, in case there's some other way to achieve these goals: 1) Building in the Flash IDE is really slow; I was hoping a third-party compiler would be faster. 2) It would be nice to be able to build projects on machines that don't have the Flash IDE installed. I'm familiar with other AS3 compilers that are out there, but I don't know of any that take FLA files as input.
There's a plugin for Eclipse called FDT. It uses the open source compiler MTASC and supports ANT. The tool is free for OpenSource developers. Get more Infos here: http://fdt.powerflasher.com/
Hope it helps :)
I also recommend using FlashDevelop. It's another open source tool that's a very lightweight IDE (SciTE based I believe) that integrates SWFMILL, a popular tool which can create SWF layout items from XML files, and mtasc, a popular third party compiler for Actionscript. I am not entirely sure you can take .FLA files as input, but you CAN avoid FLA files altogether by creating the layout in XML, or if the designer / Flash Developer who creates layouts for you can simply provide a compiled, empty (as far as code) SWF file, these tools will allow you to inject compiled actionscript directly into the SWF file. This technique can also be used on the command line to generate build scripts and so forth.
Here's the website: http://www.flashdevelop.org