Let's Encrypt vHost config broken
After activation of Lets Encrypt in 3.1 every generated vHost (Apache 2.2, CentOS 6) is broken afterwards because there are no newlines in the generated vHost file:
RewriteCond %{REQUEST_URI} !^/\.well-known/acme-challenge/ RewriteRule ^(.*)$ [...]
Therefore only an .err config is generated and further changes are taking no effect.
It seems the problem ist located in /usr/local/ispconfig/server/conf/vhost.conf.master
.