Using custom HXML compilation rather than FD's

You can use a custom .hxml file to build your project in FlashDevelop.
Go to Project -> Properties.... Choose Custom Build as compilation target. Go to the Build tab and insert the following line in the Pre-Build Command Line field (assuming you named your build configuration compile.hxml and placed it in the root of the project directory):

$(CompilerPath)\haxe.exe $(ProjectDir)\compile.hxml

Click OK. Whenever you compile, test or run, FD will use your hxml file. You can even edit .hxml files within FlashDevelop.