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That said, I think the Dataview plugin is the answer to your problem with your file structure. The thing that stresses me out about top-down hierarchical structures is that a lot of the times, you could categorize a file into many different categories. However, as long as you label your metadata, you can easily find that file from any conceivable category. This video explains why dataview is so useful (this person also writes a lot of DND campaigns, so her techniques may be useful for your kind of writing). This other video also can help explain things.
You may also like this plugin: mindmap.
And the breadcrumbs plugin may also be useful for you since you seem to like to have hierarchical organization.
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