All you need is links
It might be interesting to contrast with what my own website has evolved. Discussion: https://www.gwern.net/DesignHere the idea is not so much 'links are you all need' as transclusion is all you need, in the form of dynamic popups/popins.How can we have a ridiculous number of references? Make each one popup its metadata like an abstract. How can we have a ridiculous number of WP links for every term and concept? Pop them up, WP has an API. How can we cross-reference sections or arbitrary /s within a page? Make it popup. How can we cross-reference other pages without the dreaded hypermedia effect of "oh my god each page is 1 sentence long and I have to click through a thousand of them, screw you man"? Pop up with a mouse hover, effortless and fully recursive. How do we support backlinks, or indeed any arbitrary kind of metadata page about a link we may wish to create at some point? Just generate the HTML snippets and link to those snippets - popups do the rest. How do we implement tags? You'd better believe it involves simply creating a HTML page with all of the links with the 'tag' and then simply linking to it! How do we do topic-modeling with the coldstart problem of requiring heavy manual curation of all links (which is what OP suggests as a replacement)? Use topic-modeling to generate link suggestions while editing, and then link the useful ones (thereby making them visible when you edit and also generating backlinks automatically). When we can pop up anything, we can pop up raw data files like PDFs, or their syntax-highlighted versions (source code); we can even pop up pages on other domains (subject to a whitelist of having checked that X-FRAME headers don't kill it and it doesn't otherwise break horribly inside the iframe).