So it sounds like you want to keep using Quillpad, and so you’re stuck with the folder structure, which is no subfolders, that Quillpad implicitly requires.
It kinda sounds like you need some way to “tag” your notes so that whatever application you’re using would pick those up and be able to give you all notes with a particular “tag” in a view.
If that’s the case, Obsidian can do that. You can keep the current folder structure (of just being a flat folder), and add tags to your notes (e.g. #my_tag). Then, instead of using the default file viewer, you’d look at files via tags. The only problem, though, is I’m not sure if there’s a particular view that can do that.
And no, Vim wouldn’t do what you want either, at least OOTB, cause it’s just an editor and not a file organizer or indexer. Pretty sure that applies to Emacs as well. You’d need some plugin that would do that, and I don’t think I’ve heard of one that would do this.
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