ensure CLI commands are registered

[Matt Lewellyn]

Ran into an issue with the assets command from Flask-Assets. The FA module is loaded by app setup, so the command is discovered. If we run <app> --help-all the assets tree and help are included. But try running <app> assets and the result is "command not found."

Turned out the issue was that keg sets up a "primary" CLI group and runs that, so any other commands need to actually be registered on that group.

Need to figure out how the command is finding the help, as we may be able to use that to register any other commands onto the main group.