It's almost a "hidden feature" currently, but near the top of the Markua manual we say:

"Markua is a plain text format. Markua is basically Markdown, minus all inline HTML except comments, plus a number of extensions to support everything you need to write a book or create a course."

So, this means you can do comments in your manuscript that won't appear in your book, like this:

%% This comment in the manuscript will not appear in the book

You can also do this:

<!--This comment in the manuscript also will not appear in the book-->

So, if you type this in your manuscript:

This is what you will see in your book:

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