What about tags? 5+ years ago I used tags, but now I mostly use links. Links work better for me because they take me to a note rather than a search. I like this Wikipedia-like flow better, because it keeps me in context of my notes.
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This is similar to how I used tags, then moved to tag pages, and now I don't bother calling them tag pages anymore... they're just pages. I write a little bit about this in tags vs pages
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working note - Tags are an ineffective association structure