I've taken a look at the Folders lay-out and it's ok as far as a filing system goes, however it doesn't deal with the problem effectively.
If you click on a folder you simply get a list of all the pages in that folder and there isn't any order behind it. If we created a new sidebar with the folder names as categories you would then have to recreate sub-pages with the relevant links to the wiki page - but this system is already in place and therefore it becomes unnecessary and time consuming work, notwithstanding human error in this process. For instance I looked at the folder Collected Works and it takes me to this :-
Collected1.JPG (26.01K)
Number of downloads: 0
when it should really take me to this :-
collected2.JPG (43.51K)
Number of downloads: 0
and this is just one small collection of pages.
I know you didn't create the title I find it baffling that all the information on some of the most important aspects of the books such as the Tiles, Warrens, The Deck etc are under the heading "Miscellany" - like this:
miscellany.JPG (37.37K)
Number of downloads: 0
This is a screenshot of the sidebar from my own wiki - it is the one on which the site wiki was originally based. All the files currently on the wiki are already accessed from these main headings - the links were simply renamed - therefore making changes to this structure will be much simpler - links can be changed and structure pages can be renamed, without having to start all over again. You will probably find that your folders will fit easily with most of these categories as your folders have similar names - so you must have liked something about it
sidebar.JPG (67.83K)
Number of downloads: 0
I appreciate that there are a few things that will need to be renamed or categories that could be added or taken out - for instance we obviously need the FAQ and Book Summaries etc, but it will be much easier to add those to the sidebar and link them to the correct page than to try and re-organise the structure altogether. I think this is a good opportunity to tidy things up, as you are currently doing (and a lot of work I know), to try and reflect what's in the folders within the category headings.