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.