Nate's right. You CAN override the standard Maven directory conventions, but you'd probably regret it. I don't like them myself, but at least they're a standard that anyone can come in and take over the project with minimal learning.
The standard project structure for a JAR project looks something like this:
If you explode your dependency classes and put them in the main resources directory, they should copy into the final jar.
How you get them exploded is up to you. If you are working with a fixed set of jars, you can put them in a library directory, write an ant sub-task to explode them and let Maven take over. If you're attempting to use Maven-managed libraries, you'd probably have to do more work (or copy them into the above-mentioned library source directory).
There MIGHT be a jar-combiner Maven option, but I don't know of any. Not that that means much. [ February 05, 2008: Message edited by: Tim Holloway ]
An IDE is no substitute for an Intelligent Developer.