We have a fork of HTMLBook called TextbookHTML, and my intention is to get that completed by Books in Browsers. As much as possible we are trying to be compatible with HTMLBook. And Phil and I have been in contact with Adam Witwer who is leading that project and he is even interested in changing things to be more compatible with us when it makes sense. For instance, we want foot/end notes to be defined next to the content they are referencing. And Adam indicated they would be willing to do that instead of physically placing them where they might get displayed.
The points raised about HTML5 as an authoring and output language are exactly what we are trying to achieve! Hopefully github-book can become the open-source way of authoring books in HTMLBook and TextbookHTML.
Kathi
(See Marvin's links below)