[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
[ADAM-327] Adding Gene, Transcript, and Exon models
Testing and test files.
[TO BE REMOVED] BIG test files.
Added the Alphabet trait and DNAAlphabet implementation.

Updated BlockExtractable to take an Alphabet parameter, and to use the DNAAlphabet by default.
Removing the Gene object, per Uri's suggestion.
Removed Extractable trait on Transcript, and replaced the method with three different methods (again, per Uri's suggestion) for extracting transcript-related sequences.
Upgrade bdg-formats version to 0.2.1-SNAPSHOT
Example GTFParser using the Feature2 schema.
wip
wip