org-roam-bibtex VS scimax

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.

Scimax should have out of box setup for bibliography, references etc. Anyway, regardless of what you use Emacs for, one step a time, would be my recommendation. Just start using it and solve problems as you experience them. It is better to add a single thing at a time when you need it, than to add 1000 different things because you think you will need them, and then not know what you have or what causes a problem.

https://github.com/wdavew/org-excalidraw is close. I discovered you can install Excalidraw from Chrome, and then it is like a local program. That is pretty amazing in itself. org-excalidraw indeed offers an org-link and way to make an excalidraw file from emacs, edited natively in an external excalidraw window. The svg preview does not work though if you use freehand lines in your image, and I was unable to install the npm packages on my Mac for some uninteresting reason related to DNS, but it did work in a node docker image. I find writing in excalidraw less advanced than in tools like Notability or PDFExpert. There are some artifacts in excalidraw from smoothing, or dangling pixels that I don't love. I forgot I had previously used https://github.com/lepisma/org-krita. Krita is a full drawing program, and this integrates into org-mode with image previews nicely. I am not that skilled in using it, and as a full drawing program, it has a learning curve. I wrote https://github.com/jkitchin/scimax/blob/master/scimax-inkscape.el to integrate inkscape into org-mode. It works, but I find inkscape slow to open, and I am not that skilled in using it.

Maybe give scimax a go?

Anyway, if you want something geared toward scientific usage, there is Scimax by J. Kitchin. There may be some others, but I am not aware off.

Apart from the ones already mention, John Kitchin's science-focused Scimacs is also an option.