Obsidian lets you live on top of the filesystem structure using markdown files, and it gives you links, tags, topic clouds, and more.

If you use it with reasonable conventions, you can compile and deploy a web version with ghost or zola or something automatically run in CI.

It's backed up, synced, and comes with desktop and mobile apps. It has vim key bindings and git plugins.

It's a pretty sweet system that works nicely with Unix, and it adapts to multiple navigational and organizational paradigms.

I've tried a lot of things, and nothing has ever come close to Obsidian.