scope Caller and Arguments inside companion object

this makes for a messy diff but sets up the auto-parsing of cmd-line
args for Guac commands
fold Args4j.apply into Command
make Command inherit Serializable and Logging
add GermlineCallerArgs
unroll wildcard guacamole imports
add SomaticCallerArgs
provide SparkCommands with SparkContexts
add SparkContext.stop() to SparkCommands
update “variant caller” language in Command
wrap sc.stop() in a try/finally block
Merge pull request #245 from ryan-williams/command

Move Command boilerplate into SparkCommand
import nits
upgrade: spark1.2.0, adam 0.14.1, bdgformats 0.3.2
fix deprecated use of SAMFileReader