Refactor CLI handling (#1368)

* Rework cli handling

* Update readme

* Adds support for custom subcommands and extra run parameters

* Update readme

* Fixes compilation after master merge

* Make "Run" the default subcommand

Actually its hidden to the outside that is an subcommand.

* Rewrite CLI to work without breaking old CLI behavior

* Some cleanup

* Fix incorrect config setup

* Update README

* Fixes after merge

* Fixes incorrect README