[Agama]

The "#" characters are important as they indicate an anchor within the current page in HTML. The rest of the link id is up to you. I used "n" prefix to link to a note, and "r" prefix to return from a note.

I have now attached the ePub which results from conversion.

You may well want to style your link references to make them look better, e.g. superscripts or within brackets, but be careful not to clash with Markdown.