For those who are wondering why sschueller is saying such things (when I first read his comment my reaction was "how the f* could this be limited to Apache?", which worried me since I mostly use lighttpd), see the How It Works page [1] of Let's Encrypt.
> I would rather have the client just output the certificate and key in a dir
> I would rather have the client just output the certificate and key in a dir
Could not agree more.
[1] https://letsencrypt.org/howitworks/