Resource overlays might have solved the problem a bit More gracefully. They allow you to specify additional resource directories that take precedence over the default one. I don't have a link at the moment, but google should be able to tell you something. You'd still have to hack around with the build file a bit, but if you're a java/android programmer you should know about ant anyway.

As long as you're learning about java build tools, take a look at the android maven plugin. It can be useful once you outgrow the confines of the default android build process.