Refactor CLI with subcommands

[bamthomas]

Is your feature request related to a problem? Please describe.

By now datashare CLI is implicitly handling subcommands:

• index
• scan
• NER extraction
• NER extraction server
• HTTP server
• CLI services

But they are mixed in the numerous CLI options with inconsistencies.

Describe the solution you'd like

I would be convenient to have an exhaustive list of these subcommands and a specific help for each of them with options,

Additional context

It seems that it is not possible with joptsimple. There is a list of command line parsers here

We had considered JCommander in previous discussions.