This creates the directory where we clone the latest letsencrypt. Then we start the manual process to create certificates.
A terminal application will start asking you for your email for correspondence (although you'll not need to check your email to do anything of this), and the domains for which you want the certificate.
Then it'll break out of that and ask you to create a file on your publically available site for it to check.
Once that check is finished, it'll output the certificates to /etc/letsencrypt/live/yourdomain.com.
Now your existing /etc/apache2/sites-available/your-file-name.conf should look something like