How to use Github Pages with Dependencies?
You can consider your gh-pages branch more as a server than as a git branch - so many of the common rules for git branches don't apply there.
It's not uncommon, if you are developing an application hosted on GH:Pages, that your gh-pages branch is full of auto-generated content - exactly the opposite of what you'd do on a normal git branch, in which you don't version generated resources.
So it wouldn't be uncommon to have some build process that generates the contents of the gh-pages branch. You can learn a bit about how Learn Git Branching does the trick, for example, or read the Jekyll on GitHub Pages docs to get a better insight.