Don't stop Apache until we have to; start it again right after.

roles/common/files/letsencrypt-gencert

 #!/bin/bash
-service apache2 stop
 d="$1"
 for i in www mail autoconfig read news cloud git; do
   if (getent hosts $i.$1 > /dev/null); then
     d="$d,$i.$1";
   fi
 done
+service apache2 stop
 /root/letsencrypt/letsencrypt-auto certonly -c /etc/letsencrypt/cli.conf --domains $d
+service apache2 start