came across this project the other day:
https://github.com/ahrm/sioyekit's basically a minimalist pdf reader with some enhancements for reading text books and other academic-ky stuffs like the ability to jump to a references or figures mentioned in a paragraph even if the author didn't bother linking them, open a popup so you can view those without losing where you are in the page, etc.
it's not perfect tho: so far my biggest gripes is the inability to add popup note-type annotations and the lack of integration on any reference management platforms (which is just baffling).
