CLI Development Overhaul

CLI needs an overhaul. Currently it uses a series of sub-commands, but this scales poorly and is difficult to use. A complete overhaul is possible. The only necessary command from the CLI that must be retained it the dump-to-plain-file utility. For user facing upload functionality, CLI should be developed and make use of a configuration file in some standard markup language (XML, JSON, YAML etc.). This handles all the inputs to the pipeline and should call the pipeline via the workload manager.