I have a single server that I use to host a whole bunch of smallish websites. It's recently come to my attention that a service called LetsEncrypt allows me to get an SSL certificate for free. The catch, as far as I can tell, is that they don't allow you to do any traditional SSL setup and instead you must use a script they provide which automatically requests a certificate for your server and configures apache for it. The problem, now, is that their setup script does not support the fact that I have 8+ virtual hosts all in my single 000-default.conf file for apache.
So my question is, how do I configure apache to read multiple site configuration files so that I can separate my different virtual host definitions into different files?