The publish_production.sh script uses awestruct --deploy to publish the site. Normally it should do something like this:

git checkout master   
cp -r _site/* .   
git commit -a -m "Published master to GitHub pages."   
git push origin master  

Instead, it deletes everything on the master branch and pushes that, taking the site down (because GitHub relies on a CNAME file to find the domain name). The solution is to revert the commit (since some files are not generated) and publish the site manually.

This could be caused by an incompatibility between the version of git on the CI machine and the 'git' gem used by awestruct.