[ADAM-356] Refactor packages for org.bdgenomics.adam.rdd contents

o Moving indel realignment code into a consistent package.
o Moving read specific RDD transformations into a new rdd.read package.
o Move SummarizeGenotypes into the rdd.variation package.
o Moving pileup aggregator into a new rdd.pileup package.
o Breaking read RDD functions/context into rdd.read package.
o Moving contig rdd functions/context into own rdd.contig package.
o Moving pileup and pileup RDD functions into own rdd.pileup package.
[ADAM-369] Improve debug output for indel realigner