[shurcooL]

I understand the problem, I'm thinking how to best solve it.

FWIW, the markdown files for all chapters in that book you've linked do not contain an extra newline at the end; there's only one (just like markdownfmt leaves it).

What about using something like cat, except one that inserts a newline between all the files it concatenates? That way the .md files can remain as they are.

[heinrich5991]

You could also terminate each paragraph with a double-newline, instead of using that to separate them. That would fix the problem.