Make `CLI` behavior and output to match latest conventions

This updates the `CLI` behavior and output to match our latest
conventions. This includes a few small changes:

* Only output the version number when using the `--version` flag.
  This makes it easier to parse the actual version number and
  doesn't hurt the readability.
* Fix a minor behavior problem with only passing a config file.
  When this was done, the CLI would use the config file as the
  command instead of assuming `run` for the command and using
  the config file. This corrects that behavior.
* Update the output of the help message. This is a better
  explanation for using the command and matches our latest
  conventions.
* Code/Test cleanups and updates to match our latest conventions.