The WebPageTest server updates itself directly for git by running git pull origin master in the cron. One problem for us is that we have edited the ec2_locations.ini file and when we run and update that files is marked as modified:
git status ... modified: ec2_locations.ini ...
If that files is updated in the repo, it breaks our build. We should look into how best add our own changes (I guess easiest by looking at the .gitignore file to see what files that are supposed to be ignored and find the update pattern, since we are missing docs).