There may be other unforeseen breakage primarily in the handbook portion of the wiki.
The Table Of Contents section of each "PC-BSD® Users Handbook" page may be the best workaround.
This control panel chapter should include an AppCafe® section. The Series chapter that Using AppCafe® is part of, should be distributed into other areas of the handbook. A new series chapter, The Commandline Method to be placed nearer the back of the handbook, containing another hierarchy of all areas previously described with the cli commands and how-tos. Each location in the earlier chapters where those sections/chapters had been, will have a link pointing to the location in the new series chapter. (I would say page if every title in the table of contents resulted in exactly 1 8.5x11" page, and so I created a new name to describe it :)