I've managed to push files to the master branch of my repo as well as a second branch called gh-pages. When I launch mysite.github.io it shows the contents of the master branch. Is there a way to redirect it to gh-pages instead?
I'm doing this from the Mac terminal.
It sounds like you're confusing User / Organization pages with Project pages.
User / Organization pages live in a specially named repository called username.github.io, and publish from the master branch. They can be browsed at http://username.github.io.
Project pages can be part of any repository, and are published from the special gh-pages branch. They can be browsed at http://username.github.io/project-name.
If you want to have a project page, make sure that your repository is not named after your GitHub user name. If you want your project to be available at http://username.github.io, you must have a User / Organization Page, which must publish from the master branch.
