(+automatically insert footnotes someplace. probably similar to pdf annotations. user can chose to embedded footnotes somehow to make clicking them work across page. Or maybe use a different mechanism altogether.)
Agreed. I use this feature extensively, and often in an iterative way: I frequently rearrange blocks; retroactively clean up earlier blocks by moving some of their content into footnotes; add references and extra resources here and there; etc. It’s quite laborious having to swap indices (my most commonly used system) both inline and in the footnotes section (four tasks per swap at minimum).
Would help a lot if a list of notes and references could work similarly to numbered lists in that if you add a new entry, index numbers update accordingly (and then the corresponding inline links would be updated automatically).