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)