Cross-referencing
Cross-referencing is done terribly.
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All the academic cross-referencing formats are pretty awful. None of them are particularly powerful and there's so many opinions about the correct way to do it, they become worthless.
No child categories.
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I'm thinking -- the "A" tag in HTML was meant for referencing -- but most of the time, we do not include a proper semantic relationship, other than link title (but we could, if we had a list of commonly used semantic links). For example, Wikidata P is a list of such link types (they call them properties)...
But then, URL itself as such was meant for referencing, so why shouldn't a URL include semantic link data.
And then, usually URLs are long, if you want to reference things in plain text (rather than hypertext).
These are certainly challenges in cross-referencing.