While organising my papers using :
I wish tagging systems had 'implications' between tags. So if I add a more specific tag to an item it implies the more general ones too. Eg. I'm tired of adding 'Algebraic Effects', 'Effect Systems', and 'Effects' to the same paper…
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Note that it is not a strict hierarchy - more like a graph. Like 'Algebraic Effects and Handlers' implies 'Algebraic Effects' and 'Effect Handlers'. And the implication should run the other way too, if I have the two latter tags I should get the former.
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Another idea: you should be able to get suggestions to apply more specific tags (in case you forget that you made more fine grained tags, which is common if you have lots of them).