Maybe try Write?
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This is what I used for math lectures.
This app can be configured to produce plain SVGs which can theoretically be embedded into org-mode documents and can easily be stored in git. I have always used it stand-alone though.
It's proprietary and the UI looks like an Android app from 10 years ago but it's the best hand-drawing experience I've found on Linux.
If you use org mode, you can use this https://github.com/misohena/el-easydraw. Its a basic drawing tool in emacs.
Xournal++ should work well
Gilles Castel (RIP) published a couple articles on taking math notes with Vim + LaTeX which I found eye-opening. In another article he posted about how he integrates Inkscape into the process. If you haven't read the articles, they may be helpful for what you are doing.
Never used it for notes, but yes inkscape. Inkscape is much more stable than it was in the past imho.
It was this comment where I learned that Gilles Castel had passed away :/ what a loss
That's pretty amazing. His notes look like textbooks.
Have you checked out Xournal++ already?
Xournal++
It looks great, I'm definitely gonna try it!
Thanks!