How do I configure GitHub to use non-supported Jekyll site plugins?

Depending if you deal with a User/Organization (UO) site or a Project site (P), do :

from your working folder git init
git remote add origin [email protected]:userName/userName.github.io.git (UO) or git remote add origin [email protected]:userName/repositoryName.git (P)
jekyll new . creates your code base
in _config.yml, set the baseurl parameter to baseurl: '' (UO) or baseurl: '/repositoryName' (P)
in .gitignore add _site, it will be versioned in the other branch
jekyll build will create the destination folder and build site.
git checkout -b sources (UO) or git checkout master (P)
git add -A
git commit -m "jekyll base sources" commit your source code
git push origin sources (UO) or git push origin master (P) push your sources in the appropriate branch
cd _site
touch .nojekyll, this file tells gh-pages that there is no need to build
git init init the repository
git remote add origin [email protected]:userName/userName.github.io.git (UO) or git remote add origin [email protected]:userName/repositoryName.git (P)
git checkout master (UO) or git checkout -b gh-pages (P) put this repository on the appropriate branch
git add -A
git commit -m "jekyll first build" commit your site code
git push origin master (UO) or git push origin gh-pages (P)

You now have something like Octopress does. Look at their rake file, there are some nice comments inside.