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)
what file is going to be ingested, also that a file can be on the local filesystem or hdfs. see the current README in geomesa-tools for more details.