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If you really like your hierarchy, you can more or less imitate it with a hierarchical field in Calibre. I use a custom Path field that works like a system of nested subfolders in the Tag Browser. (Although in hindsight I should have called it something else because there's already a Path in Calibre. Still, it hasn't caused any conflicts yet)
Calibre won't assign this custom field automatically though, so you'd have to enter each book's "path" manually.
But it sounds like you're not too stuck on your folder/subfolder system anyway.
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