So Zim-Wiki with the Backlinks plugin, then. Notes (wikipages) are stored as ordinary text files in a directory structure that is whatever hierarchy you've used

So Zim-Wiki with the Backlinks plugin, then. Notes (wikipages) are stored as ordinary text files in a directory structure that is whatever hierarchy you've used in the notes. (I tend not to use hierarchy much for my every-day notes.) Zim doesn't use Markdown as it's native or input syntax, but can copy text as md if you so wish. Honestly one of the most underrated, understated tools I've ever come across, and one I would hate to have to live without.