The maven.ear.src directory can not be the root of the project.
If maven.ear.src is set to the root of the project, Maven will improperly package the dependencies in the EAR (the "tmpEarDeps" directory will get mistakenly included in the EAR as well as other root level files that don't belong in the final EAR endstate). This presents a problem because RAD (Rational Application Developer - i.e. the new version of WSAD) requires the META-INF directory to be at the root of the project. Therefore, since Maven cannot have it at the root and RAD requires it to be at the root, we have to rearrage the directory structure arround each time before we build the EAR to satisfy Maven. We copy the META-INF directory to a temp folder that is not at the root of the project. Then, we set the maven.ear.src to point to the temp folder. This current workaround is done with a preGoal to the ear:ear goal.
There has also been a bug/enhancement logged with RAD as it should be more flexible as well.