Yesterday, after a simple commit, my entire site went down. I spent entire day troubleshotting the issue. In the end, the resolution was simple: change the default branch.
The GitHub Pages documentation says that you can push a file named index.html onto your master branch to make it automatically available at username.github.com
Let’s say your GitHub username is “Alice” If you create a GitHub repository named alice.github.com, commit a file named index.html into the master branch, and push it to GitHub, then this file will be automatically published to http://alice.github.com/.
What it doesn’t say that, it will not work if you have changed your default branch from master to something else. In that case, index.html should be pushed to default branch.
Since I use Jekyll with custom plugins, I maintain two branches: Source to store source Jekyll files and master for the published content. I had mistakenly set the source branch to be default rendering the whole site to be unavailable.
In nutshell, always remember that pages are always served from the default branch and not master branch.