Also, I would avoid linking to 'master' as it's a moving target (in the future such a link could point to completely different code or even a file that doesn't exist). I try to link to the actual commit that master is pointing to at the time: https://github.com/h5bp/html5-boilerplate/blob/7a22a33d4041c...
What are you talking about? How? What? Are you sure you mean 'bootstrap'?
Maybe it's just some feature of bootstrap I don't know about, but I'm not even sure what to go looking for because I'm not sure what you're suggesting is built into bootstrap. Built into the Javascript parts of Bootstrap somehow? What is, exactly?
How/Where? I've had exactly this problem and have had to shim (requirejs) bootstrap with jquery cdn + fallback paths... ? It certainly doesn't resolve its own dependencies under AMD