Forgot the link to Zotfile in the previous post: http://zotfile.com
Yeah, you’re asking the key questions. You’ll find many approaches to the problem you’re describing here, on the Bookends forums, and elsewhere on the web. There isn’t really a right answer—the key is to iteratively develop a system without spending too much time on the system, hah.
That thread details my approach. In my opinion, there’s no good hierarchy for complicated topics. At the same time tagging can be problematic: https://fortelabs.co/blog/tagging-is-broken/ (though Tiago has changed his tune a little on this over the years)
So, I’ve tried to reduce friction by saving everything in the same way and relying on search and a closed tagging system (e.g., don’t tag openly—predefine tags and use automations to only choose from those tags).
On reflection, though, I haven’t actually used those tags since I started maintaining them months ago. Like, at all. There’s always a possibility that’ll change, so I guess it provides some peace of mind. Still, I find I can usually find what I want because I remember authors’ names and paper titles. So I think I would advocate for using my automatic-organization-into-semesters-by-year approach and just use search. Don’t worry about other organizing paradigms.
I have also recently gotten into the PKM world, and while there’s a whole other chaotic class of apps, systems, and workflow questions there, I do think the philosophies behind Taking Smart Notes and related workflow philosophies add a valuable dimension to remembering and using the readings you’re using.
Finally, on Zotero vs. Bookends: honestly I’d stick with the former. Bookends is more powerful and fluid as a Mac app, but Zotero was definitely fine, and I think if I’d gotten better with Zotero and citekeys I wouldn’t have felt the pull for Bookends.