I'm using HTML5 boilerplate, and saw that they're separating jQuery from main.js and plugins.js. I understand that the logic behind this is that a lot of sites use jquery and if you use a cdn there is a big chance that the user will already have it cached.
But since my use of html5 bp utilizes a build step, I could also concatenate and minify jquery with all my other scripts. So:
From what I understand HTML5 BP doesn't consider the concat/minify option since their boilerplate doesn't include a build step. But since it is an option to me; is there any hard data about what is the best option here, or what the real world differences in performance are?
There was a large discussion of this (and other related issues) in a pull request last year. You should check out that thread. Lots of detailed discussion.
The reason H5BP uses that set-up is that it's the best default solution. If a user of H5BP doesn't do anything else to their set-up, they're guaranteed to get a geographically optimized version of jQuery served to their users from a CDN source with the highest possible chance of hitting the cache lottery.
Beyond a default solution:
Really, though, testing your set-up against your own geographical audience is the best way to go. It's the only way to answer this question for your site or application.