In our team we are using Gradle for our projects that are based on libgdx and android. When we transitioned to the Google Android plugin for gradle we had kind of a hard time to migrate our setup.
I have written an article/tutorial documenting how we solved our problems and the final setup we used that has been posted on our site.
I though I might share it also on this forum in case it might be useful.
You can find the tutorial here