Clean up $wgExtraNamespaces in InitialiseSettings.php

Doing a bit of clean–up:
1. Sorted wikis by family (type) and then alphabetically;
1.1. Includes a todo for Wikivoyage wikis
2. Removed an empty array for incubatorwiki;
3. Removed some empty lines and fixed in–line comments;
4. Fixed a commented line I inserted by mistake when submitting
   a patch for Meta-Wiki upload bug 50287

Bug: 50658
Change-Id: Ic54cf4faaaaee9c1e850a5fe00f6fe18fb30b8f9