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)
ohhh i think the diff messed up...this block (line 163) is part of the `describe` command... for ingest `--file` is gone and is now a "main parameter" in order to support ingesting multiple files in a future ticket...usage is now `geomesa ingest [options] filename` I updated the readme