/usr/share/desktop-directories/X-GNOME-SystemSettings.directory is in gnome-menus 3.13.3-6.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 | [Desktop Entry]
Name=System Settings
Icon=gnome-settings
Type=Directory
NoDisplay=true
|