I prefer to keep it simple. I add references in my .bib database via Zotero, then I version control the .bib file (exported from Zotero). And then I add .md files with notes, and the .md files are named according to the citation key in the .bib file. Then I version control those .md files. Advantage is that notes are all in the same format and place, regardless of what reference type (e.g. pdf, webpage, could even cite a video), and they are all very easily searchable, including through time (via version control).

EDIT: I keep a separate folder on my Dropbox (so not version controlled) of the actual resources, such as .pdf files. Again named according to the citation key in the .bib file.

you might wanna have a look at pubs [0]. It is a command line bibliography manager.

The folder structure looks like this:

  ~/.pubs/
      bib/
      doc/
      meta/
      notes/

The bibkey is the filename for the different files in those folders, and for notes you can use markdown. You can then keep your pubs folder under version control (or symlink the (sub)folder(s) to wherever).

[0] https://github.com/pubs/pubs

Thanks, that looks really interesting!

On Mac OS X, I like 'Highlights' because it permits exporting PDF notes into a Markdown file. I then keep all the notes in one large file---which I admit is far from optimal but still easy to search, index, and query. Would be interested what other people think about this.

I searched for this but it says it is coming soon: https://highlightsapp.net/

Did you mean something else?

No, that's the one---but they just updated to a subscription model, which I was unaware of. I have the 'boring' normal version of the app still.

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

The article doesn't mention it but entries can include an "annotate" field. I use it to add short summaries and notes. It is not used by the standard bibliography styles, but it can be used to produce an annotated bibliography.

Never used it myself, though, except for detecting my name in a bibliography and highlighting it (for publication lists and some such).