Hi all,
as I just created about 30 certs with the certonly option, the folders /etc/letsencrypt/archive/domain-0001 and /etc/letsencrypt/live/domain-0001 were created probably because I tested it before with the --staging option. To avoid this behaviour, I had already removed the archive/domain and live/domain folders before, but it seems not to help. How can I prevent this? The Apache virtual hosts are also created automatically by my script and now manual changes are required for the Cert directory of the domains, where a staging cert was created before, which was not my intention.