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It would be extremely barebones, but you can do something like this with Pandoc.
I think I looked into this before and it lacked a feature, but I don't remember what it was. I might be getting it mixed up with another tool. There were a lot of tools that almost worked but were focused on making books with ordered pages rather than a tree. I think gitbook was one.
For folks interested in following in my footsteps, eleventy didn't fit because it couldn't convert relative links to markdown files to relative HTML links to the HTML files (out of the box, probably possible with plugins).
This just feels like such an obvious thing there would be a tool for but I can't find one. Even most editors that render Markdown as a preview can do this out of the box.