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One problem I see in note-taking systems is finding the threads through them. After a certain number memory is not reliable enough to know whan where you've left off on a certain overarching topic.

Curating good metadata on your notes is crucial, but it is easier said than done. Hillel Wayne has a nice write-up on tag systems.

It is also a question of the workflow. Is tagging part of the writing, or were it better done with a bit of distance? The latter would have charme, as you have more context and can be in a different state of mind when you do it. It is easier to cluster two dozen notes into three or four buckets, than coming up with a proper tag at the time when each note is written. Keeping the tags seperate from the tagged note itself would also allow to refactor the metadata without touching the notes themselves. But would that get done at all? It should also not be too hard to make up a tag while writing. Anyway, tags are not a trivial design decision at all.