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
double-dash, dash-case all command-line options
drop unused PoCIndelCaller

fold PoCIndelCaller’s tests into SomaticStandard’s

fixes #207
Merge pull request #250 from ryan-williams/args

double-dash, dash-case all command-line options
Merge pull request #251 from ryan-williams/indel

drop unused PoCIndelCaller
pass reference base to pileup instead of rebuilding; drop saving of mdtag
test fixes; updated cigar/sequence to match mdtag in test reads