If you're familiar with command-line git, it's straightforward to manually add a new set of Project Pages.

Make a fresh clone

To set up Project Pages, you need to create a new "orphan" branch (a branch that has no common history with an existing branch) in your repository. The safest way to do this is to start with a fresh clone:

git clone https://github.com/user/repository.git
# Clone our repository
# Cloning into 'repository'...
# remote: Counting objects: 2791, done.
# remote: Compressing objects: 100% (1225/1225), done.
# remote: Total 2791 (delta 1722), reused 2513 (delta 1493)
# Receiving objects: 100% (2791/2791), 3.77 MiB | 969 KiB/s, done.
# Resolving deltas: 100% (1722/1722), done.

Create a gh-pages branch

Once you have a clean repository, you'll need to create the new branch and remove all content from the working directory and index:

cd repository

git checkout --orphan gh-pages
# Creates our branch, without any parents (it's an orphan!)
# Switched to a new branch 'gh-pages'

git rm -rf .
# Remove all files from the old working tree
# rm '.gitignore'

Tip: The gh-pages branch won't appear in the list of branches generated by git branch until you make your first commit.

Add content and push

Now you have an empty working directory. You can create some content in this branch and push it to GitHub. For example:

echo "My GitHub Page" > index.html
git add index.html
git commit -a -m "First pages commit"
git push origin gh-pages

Tip: After the first push, it can take up to ten minutes before the Page content is available.

Load your new Page

After your push to the gh-pages branch, your Project Page will be available at username.github.io/projectname. Enterprise Pages will be available at username.[domain]/projectname. To set up a custom domain for Pages, see this article.