Alias /.well-known/ /home/letsencrypt/webroot/.well-known/
<Directory /home/letsencrypt/webroot/>
    AllowOverride None
    Require all granted
    Satisfy Any
</Directory>
<VirtualHost *:80>
   RewriteEngine On
   RewriteCond %{HTTPS} !=on
   RewriteCond %{REQUEST_URI} !^/.well-known/
   RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L]
   #RewriteLog /var/log/rewrite.log
   #RewriteLogLevel 3

   #RedirectPermanent / "https://jira.hpl.cz/"
</VirtualHost>