What is Markdown, though, if not "a format which makes a computer program happy"? Presumably, your wife was already familiar with standard typographical conventions like italics for emphasis and indents to start paragraphs. A good text processing system for a computer should let the user deal with these conventions, rather than having to learn a markup system. I'd be interested to hear why you and your wife decided to use Markdown, and what alternatives you considered and rejected.
The other alternatives were essentially opaque formats (e.g., Word or Pages) that when she & I talked about them and the amount of work that I needed to do, she agreed.
She also writes long hand, so this is a minor adaptation for her to write like she does with emails.
The changes suggested are less natural for most people, and HTML is line noise to most people. If she had to learn HTML, my wife could do so—but it isn't necessary for her to learn HTML. It's also easier for me to have to worry about clean-up than her to do so.
We do have points where we have to figure out how to make certain things work (when she has lyrics, that requires a little more massaging on my part—but I insert the bafflegab bit and she just knows to edit around it or inside it).
It isn't perfect, but the results look very good. (In fact, the second novel looks better than the first, which was laid out in Pages and took me three times as long as learning LaTeX to format the second novel. The only problem with the second novel was finding a good font for the PDF version we use as a print-ready copy.)
