I built Obsidian (https://obsidian.md/), a local Markdown file based knowledge base app. It supports internal linking and graph view, and recently added multi-pane capabilities too. It's looking more and more like an IDE for your knowledge by the day, and it's quite amazing at that.

I also wanted Obsidian to be very extensible, and the private beta community has already started extending it and it's so cool: https://github.com/kmaasrud/awesome-obsidian