[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-377] Update to Jenkins scripts and README.
Merge pull request #377 from fnothaft/register-serializers

[ADAM-377] Update to Jenkins scripts and README.
[ADAM-369] Improve debug output for indel realigner