So, I've tried every combination of dependencySets, fileSets, and copyDependencies I could think of, nothing I did seems to work. All I wanted was to have a runnable jar with its dependencies in unexploded jars (something I've done before when making a jar by hand, although I used the default package in that case, not sure if that makes a difference). When I failed in this, I tried to have a runnable jar with its dependencies exploded into a lib directory. I failed in this as well. The only thing that seems to work is to have everything exploded into the same level. I tried this briefly with the shade plugin, but have mostly been trying with the assembly plugin. I give up, Maven. You win.
I've seen this mentioned fairly often on the web. If someone has a working example of a Groovy project compiled into a runnable uber-jar, I'd love to see it.