Links are your friend. I would use folders only to separate different types of data that need different templates. For example, I have separate folders for people, places and things since I have different properties/templates for each (eg. Places include address info, people include date and relationship info). For every person/place/item/concept, create a note, and any time you mention that thing, link to the note. Later, you’ll be able to go to a note about something and see a list of every note where you mentioned it. If you use tags, limit their use for things like status (eg this note is complete, this note needs more information, etc). Links, links, links.
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