I have my apache config split into various configuration files in /etc/apache2/sites-available, not all of which are enabled. It seems to me that the Let’s Encrypt client only uses the first such file it comes across with a matching ServerName/ServerAlias, rather than checking all files and presenting an option to select which file to install the certificate into. This has caused problems where I had two config files for running different sites on the same hostname (I had one configuration for displaying a holding page, and another configuration for the production site).
Am I missing an option to tell the client which configuration file to use? And if not, could such a thing be added?