It has a bit of a learning curve but I use a combination of the emacs packages org-mode, org-ref, interleave-mode, and pdf-tools that is heavily influenced by t

It has a bit of a learning curve but I use a combination of the emacs packages org-mode, org-ref, interleave-mode, and pdf-tools that is heavily influenced by this reddit post (https://www.reddit.com/r/emacs/comments/4gudyw/help_me_with_my_orgmode_workflow_for_notetaking https://www.reddit.com/r/emacs/comments/4gudyw/help_me_with_...). org-ref is powered by bibtex to manage the bibliography and PDFs interleave-mode lets me take org-mode notes on each page of a PDF