Fixed: #4307 The new LE ssl cert paths introduced in ISPConfig 3.1.1 where not set in the nginx_vhost.conf.master

- fixed some smaller things in plugins for apache and nginx

Implemented #4271 Creating vHost Website Alias copies default index.html thus breaking the original site if it's based on index.php (or something not index.html)

- Added missing shell escaping

If you add/remove server IPs the file `/etc/apache2/sites-available/ispconfig.conf` gets recreated and it is missing the alias for Let's Encrypt ACME challenges. Copying over the current install template fixes that. 

Maybe one could remove this template duplication completely by using `server/conf/apache_ispconfig.conf.master` in the install process?

The `Header set Content-Type "text/plain"` was only in `server/conf/apache_ispconfig.conf.master` and not in `install/tpl/apache_ispconfig.conf.master` – is it necessary?

The cipher suites are only set now for ISPConfig's own vhost, the intermediate security profile from Mozilla is used here.

How to reproduce issue