After some discussion with a colleague from another company that also uses App Engine, he told me that he managed to cut down his app warm up time from ~15 seconds to ~5 seconds
I think the easiest way to do this would be to have a separate project that you write all the code in as well as store any other dependencies. When you're ready to deploy, Eclipse's export to runnable JAR file can repack all the dependencies and your classes into a single JAR file, which you would then use as your one dependency in your deployable Google App Engine project which would basically consist of any config files in the WEB-INF folder as well as other static resources + the one big JAR file.
Alternatively to the eclipse export, you can set that up as a Maven or Ant build which can also do the repacking.