I just tried following the installation instructions, however it deleted not only my project, but everything in the parent directory.
git checkout --orphan gh-pages && rm -rf `ls -a | grep -vE '\.gitignore|\.git|node_modules|bower_components|(^[.]{1,2}/?$)'` && git add -A && git commit -m "initial gh-pages commit"
I'm shell zsh, so maybe something in here which doesn't work as expected.