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by calstad 2273 days ago
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_...).

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