Does anyone have recommendations for how to read books like these? Looking for advice around note taking / annotating / skimming.
Obsidian[2] also has PDF support, where you can open a markdown document side by side with the PDF to take notes as you read. I think it also lets you highlight the PDF itself.
Emacs I think has a similar feature, via plugins/org-mode(?) to the Obsidian setup.
And of course your typical PDF reader probably has support for highlighting PDFs too, but I find them clunky and they save by exporting a PDF, which can be a bit heavy-handed IMO compared to just saving the annotations/highlights as a separate file as Xournalpp does.
[1]: https://github.com/xournalpp/xournalpp/
[2]: https://obsidian.md