Create SSL with multisite domain mapping?

I ended up rolling my own shell script to handle this myself:

# Run Lets Encrpyt
/opt/letsencrypt/letsencrypt-auto certonly --webroot -w /var/www/<root-domain>/htdocs/ -d <domain1.com> -d <domain2.com> -d <domain3.com> --email <your-email> --text --agree-tos

# Restart Nginx
sudo ee stack reload --nginx

A note on thinfs you need to change:

<root-doamin> - This is the path of the root domain from where your multisite is served. If you set-up a new site with EasyEngine for the site example.com then the root domain would be example.com

<domain1.com> - These are the names of the domains that should be included in the cert. You can append multiple domain names with the -d argument

<your-email> - Your email address. Let's Encrypt will send you a notification when your certificate is about to expire.

If you put this in a shell script you can renew your certificate whenever you want or set-up with a cron job to run every 30 days.