www-gem

There’s actually dedicated tools for this specific need like bmm and buku. Browser-agnostic bookmark managers are very nice for different purposes like multi browsers use. The idea is not to use browsers offline but to manage bookmarks outside of the browser as mentioned by OP.

Comparing to other tools they have the advantage to be dedicated to bookmark management, meaning they offer all features inherent to such task.

Yeah, there’s always a trend (like syncing everything and storing everything in a cloud), but fortunately there’s also always less known alternatives for the “weird” people :D

Bmm may be a viable option: https://github.com/dhth/bmm
I’m just not sure it can handle folders, but you could use tags as folder names to replicate this behavior ;)