org-roam-bibtex VS Joplin

In addition to org-roam, I would recommend checking out https://github.com/org-roam/org-roam-bibtex for attaching notes to specific papers that are indexed by an application like Zotero. Some good tutorials for it are here: https://rgoswami.me/posts/org-note-workflow/ and https://blog.jethro.dev/posts/how_to_take_smart_notes_org/ and https://emacsconf.org/2020/talks/17/ . Since current org-roam (post-v2) uses the normal org-mode "id" form, you can make any "headline" into an roam-registered node. You could then split your long derivations into different headlines, where the body of the headline or descriptive text could refer to prior nodes, but any latex is inserted using org latex blocks https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html . You've maybe already considered this (and I wouldn't be surprised if local references were easier to do in straight latex), but org-roam-bibtex is really nice for interfacing with your citation system for other papers.

I think you should also look org-roam and org-roam-bibtex (I can't configure org-roam-bibtex properly because I'm on Windows).

Taking this one step further, if you use the excellent org-roam package (which if you don't you should definitely check it out, its great for note-taking), there is a package called org-roam-bibtex which communicates very well with the aforementioned packages. With it, you can create bibliographic notes as part of your org-roam repository from their bibtex entry and initialize the file to also include a link to the pdf from org-noter. Once you learn it, its a very powerful and streamlined workflow for working with articles which makes your life very easy. Its quite a bit of reading to do on your end on how to make all these work together, but trust me its worth it.

Have you followed the discussion here: https://github.com/org-roam/org-roam-bibtex/issues/159

If you want to use it primarily for literature notes, maybe you should have a look at the current state of https://github.com/org-roam/org-roam-bibtex/tree/org-roam-v2 before deciding.

I've had great success with using Joplin for this, with Syncthing as a sync backend. Works well across OSes; I use it on Linux, macOS, Windows and Android.

https://joplinapp.org/

The tools to manipulate SQL aren't that bad, no.

But rather than having a self explanatory markdown & flat file, now I have to start learning about the schema & making specific tools (in my preferred language) for manipulating Joplin's schema.

Suddenly I'm digging through 20 different technic specs to decode what data is where, how it works, and what I can do to it. Want to edit history? This is the best help you'll get, pray it's adequately technical to expedite you to your purpose: https://github.com/laurent22/joplin/blob/dev/readme/dev/spec...

As I began with, I struggle to imagine anything that generates anywhere near as much user agency as flat files and markdown. Having boring common data & systems lets me apply portable skills I already have, rather than having to skill up in some particular product's own ecosystem.

Joplin is a good open source option too, feels more like the original Evernote in terms of UI/UX https://github.com/laurent22/joplin/

Joplin, an open source, extendable, Markdown-based hierarchical note-taking app: https://joplinapp.org/

It lets you choose a synchronization backend, offers applications for every major desktop and mobile OS (also has a terminal version). You can create notebooks and subnotebooks to organize your notes. You can also add tags for better search experience. I created notebooks for specific domains (work-related, home improvement, etc.) and also keep a "temp" for quick notes and W.I.P. snippets.

Its only con that it uses Electron on desktop which causes relatively slow start of the application.

done