From layout & build perspective:
GetGroups, DistCp, DistCh, & Logalyzer are being moved to hadoop-mapreduce-client-jobclient, shouldn't they go into hadoop-tools? Also there is a new version of Distcp about to be committed, should we ignore the old one and let it die.
Also, rumen stuff (which is needed for gridmix) it OK to go into main/src/java or that is a tool as well?
The MemoryCalculatorPlugin classes is being moved to src/main/java, is really required to be there? As it seems it is only used by testcases, no?
The examples POM has version in a few dependencies, they should be removed and the corresponding dependency with version should be added to the hadoop-project/pom.xml in the dependency management section.
Other than that looks good.