It might not be a direct alternative, since it's not using markdown files directly, but I really like Trilium notes (https://github.com/zadam/trilium https://gi

It might not be a direct alternative, since it's not using markdown files directly, but I really like Trilium notes (https://github.com/zadam/trilium https://github.com/zadam/trilium). It's open source, you can selfhost it and you can write your own scripts in JS to really make it your own.