Have you tried QOwnNotes? I haven’t used it but I’ve seen it, looks like it ticks everything you want.

I would also highly recommend logseq, org-roam, or vimwiki. For mobile support, definitely use syncthing (logseq has a paid sync feature, but it’s not worth it over self-hosting syncthing imo. It’s easier technically speaking, but syncthing is pretty easy too)

Logseq - I use this now, primarily because the mobile app is as great as the desktop version. Links, tasks, etc are all smooth and I love the workflow. Only reason I don’t think you’d like it is you can’t really have your own defined dir structure.

Org-roam - uses .org files that have their own syntax and such, also foss and non-proprietary though. I used it for a while because the emacs ecosystem is very robust and I use emacs a lot. Primary downside to this system is mobile support hurts, I used OrgNote for a while but just didn’t like it much. (If you go this route, highly recommend using doom emacs instead of just vanilla. Vim keybinds are the best keybinds)

Vimwiki - uses vim keybinds, love it. Same issue as org-roam though, mobile support makes me cry. There are plenty of foss mobile md editors, but none of them feel good. You can use this as a wiki via GitHub and have access to it from any web browser and make edits there as well, but it wasn’t a very pleasant workflow personally.