Running is simple... just make sure you have the following variables defined in your variables.sh file

CLOUDFLARE_API_KEY=736e6f6f70646f6767
CLOUDFLARE_EMAIL=tupac@isntdead.com
FQDN_LIST=(biggiesmalls.co www.biggiesmalls.co the.notorious.big)

then

./lets_encrypt.sh

will create (among others) the following files

• private key in ./lets-encrypt/live/${FIRST_HOSTNAME}/privkey.pem
• certificate file in ./lets-encrypt/live/${FIRST_HOSTNAME}/fullchain.pem

There's also some commented out code to copy the certs and restart nginx, but I'll leave that to you to decide how to implememt