If you're a developer who uses the GATK framework, you may have noticed that the 3.2 release broke existing third-party walkers. This happened because we had to do some codebase-wide refactoring/renaming that changes package names and classpaths (most obviously, renaming all instances of "sting" to "gatk"). We're sorry for the inconvenience but this was necessary as a preparation step on the road to providing GATK as a maven artifact.
We have posted a document that details the changes and explains how to update third-party code to work with GATK framework versions 3.2 onward here.
While we're on this topic, it seems that the IntelliJ set up instructions are a little outdated (in part due to the renaming), so we'll be updating that as well in the near future.