Test CL to use Hadoop 2.2 libraries from CDH5 repo, as well as protobuf 2.5
spacing
fix spacing
add some comments
Merge branch 'master' of https://github.com/bigdatagenomics/adam

Conflicts:
	adam-cli/pom.xml
Rewrite foldleft as aggregate to make it more parallel.
Merge remote-tracking branch 'origin'

Conflicts:
	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/rdd/AdamRDDFunctions.scala
	pom.xml