Old topic, but still unsolved!
I created a file in /etc/nginx/conf.d/includes/example.com.conf containing:
rewrite ^/$ /mail redirect;
Then ran /root/mailinabox/tools/web_update. It did not make any changes to my local.conf file. For good measure I copied the file to /etc/nginx/conf.d/includes/mail.example.com.conf (matching the hostname I use) and that did not get included either, even though there are sections in my local.conf for both example.com and mail.example.com. How is this supposed to work?