FLASC: Another open source tool in your arsenal
The tool is pretty straightforward to use, and the workflow seems smooth though haven't tried it in production environment yet.
You start by defining a project and then you can add packages and classes to it. Once a package is added, the tool recursively goes through folders and adds all of them in the project packages list, which is used in the as package parameter in the MTASC batch command.
Now, the only pitfall to using this approach (or MTASC for that matter) is no matter you use a class or package in your application, it will always be included in it if you have included it in the list of packages, while the Flash compiler will only add the classes which are being used. This can increase the file size of the application if a package, which is not being used, is large enough. However, this is a small thing to do, considering FLASC will save lot of time and frustration when compiling large projects.
FLASC has some good options like displaying the batch command, displaying errors right inside the output window.
You can find more information at http://osflash.org/flasc.