2016-07-11 11:45:03,486:WARNING:certbot.renewal:Attempting to renew cert from /etc/letsencrypt/renewal/vm31.atlas.es.conf produced an unexpected error: The manual plugin is not working; there may be problems with your existing configuration.
The error was: PluginError('Running manual mode non-interactively is not supported',). Skipping.
So I understand that if I had generated a cert manually, then I can't renew it manually in any way.
The way you renew a certificate created with the manual plugin is to re-run the original command, so if you did something like certbot certonly --manual -d example.com, you would just run that command again.
The renew command is intended only for automation (i.e. putting it in a cronjob), so it doesn’t support plugins that have to run interactively.