Fix duplicate permission lines

Patterns like `^;listen.group` will only replace the default setting during the first provisioning. Future provisionings will keep appending permission lines at the end of the file, since the semi-colon of the regexp(`^;listen.group`) won't match any lines in the file.

Applies to `listen.owner = www-data`, `listen.group = www-data` and `listen.mode = 0660`