How to get a Let's Encrypt certificate while using CloudFlare

Hello @andrewjs18,

Take a look to ./letsencrypt-auto --help webroot and you will see two options to specify a webroot per domain/domains.

Example using -w ( --webroot-path ):

./letsencrypt-auto here_your_options -w /var/www/domain.tld -d domain.tld -d www.domain.tld -w /var/www/otherdomain.tld -d otherdomain.tld -d www.otherdomain.tld

Example using --webroot-map:

./letsencrypt-auto here_your_options --webroot-map '{"domain.tld,www.domain.tld":"/var/www/domain.tld", "otherdomain.tld,www.otherdomain.tld":"/var/www/otherdomain.tld"}'

Cheers,
sahsanu