What would you like to know? In Calibre you can set regex to indicate what should be used for chapter, sub chapter etc, and it can be used to generate the TOC. So I use Markdown headings, #, ##, ### etc for chapters and subsections.
Checking, it looks like Calibre expects one Markdown file as input, where I have a few Markdown files, linking to each other in a way that works on GitHub. It looks like the sort of thing that either works as-is with luck, or is a pain in the neck and needs massaging.
