Not resetting OPTIND between each call of getopts skips all short args except the first one.
It fixes this automated command:
./certbot-auto certonly --webroot -w /tmp -d example.com --agree-tos --email contact@example.com -n
Where "-w" was parsed by getopts and not "-n"
* When getopts is called multiple time we need to reset OPTIND. Issue #3459
* Adding OPTIND reset in the certbot-auto source file
* Building new letsencrypt-auto from template
