./letsencrypt-auto certonly -a manual -d YOURDOMAIN.org -d www.YOURDOMAIN.org
for all subdomains you want to include.Make sure your web server displays the following content at
http://YOURDOMAIN.org/.well-known/acme-challenge/5TBu788fW0tQ5EOwZMdu1Gv3e9C33gxjV58hVtWTbDM
before continuing:
5TBu788fW0tQ5EOwZMdu1Gv3e9C33gxjV58hVtWTbDM.ewlbSYgvIxVOqiP1lD2zeDKWBGEZMRfO_4kJyLRP_4U
\#
\# output omitted
\#
Press ENTER to continue
/etc/letsencrypt/live/YOURDOMAIN.org/fullchain.pem
and /etc/letsencrypt/live/YOURDOMAIN.org/privkey.pem
.