I ran into this problem just now while setting up this very blog, which means we’re off to a great start.

The problem was that I needed to create a new Jekyll site, but inside the repo:

cd ~/Code/barbeque.github.io
jekyll new .

That is, the site needs to be created at the base of your repository. Most of the tutorials seem to skip the step where you create a new Jekyll site or are ambiguous about where you put it.

If you get an error about there already being stuff in the directory, use --force on jekyll new, or clean the directory out (my preference).