Thanks for these insights and listing these alternatives in one place and showing their commonalities (like tagging, hierarchies, and parsing/subdividing). One book I have found interesting along those lines is "The Discipline of Organizing". https://berkeley.pressbooks.pub/tdo4p/

Tangentially, William Kent's "Data and Reality" (the first two editions especially) also explores the larger meta-issues of moving from human-ish nuanced thinking to more limited formal representations (i.e. "The map is not the territory"). http://www.bkent.net/Doc/darxrp.htm

Coincidentally this other HN article showed up the same day: "25+ years of personal knowledge management" https://news.ycombinator.com/item?id=30903940

I have my own FOSS explorations to make software related to these sorts of themes called Pointrel/Twirlip -- but still a work in progress after over forty years. Indirectly Pointrel did in a sense help inspire Wordnet though. :-) And Wordnet was core to the rise of Google (via Adsense) which claims to want to organize the world's information (even if they may have other goals as well).