If domain has document root /var/www/clients/client2/web7, can I set subdomain for this with totally different document root (for example /var/www/stuff)? So I would end up with parent domain that has document root /var/www/clients/client2/web7 and subdomain that has document root /var/www/stuff.
The document roots of websites are defined by ispconfig, you can not set them manually. If a subdomain shall have its own document root, then create a new website for the subdomain in ispconfig and enter sub.domain.tld in the domain field.
