My tools of choice for advanced bookmarking and offline read:
* org-mode [1].
* org-board [2] for offline archiving.
* Org Capture [3] for getting links or text chunks from browser.
* git repo for tracking history.
With org-mode I can create really complex connections between articles and citations, add tags, have TODO lists and many more. To visualize things and connections, org-mind-map [4] can be useful. Because everything is text, grep, ripgrep, ag, xapian and other similar tools works without problems.
I'm aware this setup isn't for everyone (you need to be Emacs user), but I still need to find proper alternative with this amount of flexibility, keeping everything in plain text format.
[2] https://github.com/scallywag/org-board
[3] https://chrome.google.com/webstore/detail/org-capture/kkkjlf...