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
automatically register Commands with Guacamole
make Command inherit Serializable and Logging
add GermlineCallerArgs
unroll wildcard guacamole imports
add SomaticCallerArgs
provide SparkCommands with SparkContexts