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I think the .md file requirement will be redundant if @tomjemmett's pull request #25 is accepted as that uses the .Rmd format which is a bit more intuitive. If you need a chapter you just create a new .Rmd file.
It would be great to have a quick bit on how to add a proposed chapter to the book (i.e. where you "register" a .md file to be included).
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