In my wiki we use the category tree extension dynamically in a few pages to have convenient links to other pages. This means when people create new pages, all they have to do is add the appropriate category to their page and then the link will show up automatically on the master page. This saves our users time as they don't have to worry about manually adding links or link rot.
Unfortunately pages that a linked to in this way do not count under 'what links here' and therefore also show up on the orphaned page list. This makes it more difficult for the wiki admins to see if a particular page is dead/cruft that can be deleted (as usually pages with no links to them are) because it may actually be a valuable page that is only linked to via a the category tree expansion.
Is it possible for this extension to have this functionality added? I guess it would need to be configurable, as not all wikis may want this behaviour by default.