Few more tweaks to the CLI.
Few more tweaks to the CLI.

4ment/beast-mcmc,beast-dev/beast-mcmc,4ment/beast-mcmc,adamallo/beast-mcmc,4ment/beast-mcmc,beast-dev/beast-mcmc,adamallo/beast-mcmc,maxbiostat/beast-mcmc,maxbiostat/beast-mcmc,beast-dev/beast-mcmc,4ment/beast-mcmc,4ment/beast-mcmc,maxbiostat/beast-mcmc,adamallo/beast-mcmc,beast-dev/beast-mcmc,beast-dev/beast-mcmc,beast-dev/beast-mcmc,maxbiostat/beast-mcmc,maxbiostat/beast-mcmc,adamallo/beast-mcmc,adamallo/beast-mcmc,4ment/beast-mcmc,maxbiostat/beast-mcmc,adamallo/beast-mcmc