[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-372][ADAM-371][ADAM-365] ADAM Spark interaction is more canonical

Removed SparkArgs and SparkCommand
Spark config should be ADAM-independent
Added bin/ with scripts for submitting jobs to spark-submit and also using spark-shell and pyspark
Fixes #372, fixes #371, and fixes #365.
Merge pull request #374 from laserson/refactor-cli

[ADAM-372][ADAM-371][ADAM-365] Refactoring CLI to simplify and integrate with Spark model better