What is the right way to modify apps.vhost in ispconfig 3. I want to password protect my phpmyadmin path ("my-ispconfig-server.com:8081/phpmyadmin/") I added auth_basic "Restricted Content"; auth_basic_user_file /etc/nginx/.htpasswd; to my apps.vhost but after upgrading ispconfig and restarting the server, they had been removed.
You should create conf-custom directory and put your custom vhost in it as it will be used instead of default in an upgrade. But do backup this created directory and its contents especially if you intend to uninstall ispconfig as they will be deleted upon uninstall and reinstall.