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)
(picky) If the commands have been organized in the output of the command, the README.md should be updated...