At github you can have jekyll generated sites for your repositories and they will be published at <whatever>.github.io. In your repositories settings you can select the branch from which the site is built or served.

However for <username>.github.io pages, stuff has to be served from your master branch.

jekyll-github-deploy (jgd) is a shell-script wrapper that makes building your site locally and pushing the result into the master branch easy:

jgd --branch-from=source --branch=master

(That means that your jekyll sources are to be found in another branch)

Unfortunately, the README.md is removed from the master branch (where you “deploy” your site into), but that is the branch that is shown by default when people browse the repo. We are working on that, though.