Is Bootstrap mainly for CSS? Or should it be viewed as a fully-blown alternative to HTML5BP? I would love to read a guide on how to incorporate Bootstrap with other tools like HTML5BP and the Javascript framework of my choice.
Bootstrap is primarily a CSS framework with some accompanying JavaScript (jQuery) plugins to provide things like tooltips and popovers.
You can very easily use it with HTML5 Boilerplate. You incorporate it in exactly the same way you would any external CSS file. And if you want to use their JavaScript you add that the same way you add any other JavaScript.