Update nginx config for Certbot's nginx plugin

Alongside moving to certbot's nginx plugin, also use conf.d instead of
recreating the sites-{available,enabled} setup that Debian/Ubuntu uses.

Furthermore, also request a certificate for the media domain at the same
time since that's now required.

@@ -243,0 +236,4 @@
+
+If that doesn't work the first time, add `--dry-run` to further attempts to avoid being ratelimited as you identify the issue, and do not remove it until the dry run succeeds. If that doesn’t work, make sure, that nginx is not already running. If it still doesn’t work, try setting up nginx first (change ssl “on” to “off” and try again). Often the answer to issues with certbot is to use the `--nginx` flag once you have nginx up and running.
+
+If you are using any additional subdomains, such as for a media proxy, you can re-run the same command with the subdomain in question. When it comes time to renew later, you will not need to run multiple times for each domain, one renew will handle it.