GEOMESA-494 GEOMESA-523 GEOMESA-525 Replace scopt with jcommander

* Replaced scopt with jCommander
* Refactored arguments into common classes
* logged to stderr instead of stdout to support redirecting of ouput (removed stdout flag) (GEOMESA-523)
* added "json" in addition to "geojson format"
* updated readme
* Bundled SLF4j with assembly (GEOMESA-525)
Hmm... could these be defs or lazy vals?  The runner only runs one command, right?  (I.e., the initialization of all these classes is unnecessary.)