Some basic stuff for contributing here, the formatting is a bit all over the place since I have been learning Obsidian as I have been working. Feel free to go back and rework anything that you think needs it, but I think some basic guidelines below make sense. Let me know if you have any suggestions!
https://github.com/Aidurber/obsidian-plugin-dynamic-toc
I like the idea of keeping the file tree relatively flat, and letting article links do the heavy linking. However, for ease of use, I think categorizing generally things like 'Vehicles' 'Combat', and 'Matrix' makes sense. For each Folder, there should be a file matching the name of the folder that contains links to each of the files within it (See Special Actions. This supports link-based navigation through the project structure.
For each File, at the top there should be a link to the parent Folder's index file (as mentioned above) to allow bi-directional navigation. I don't think Files need to be fully atomic, but if they have several distinct components, each should use a header tag, so that section, action, attribute, etc can be linked to. See Attribute.