That doesn't stop you from changing something in your working copy. The hack here is that the working copy used to build from wasn't a clean clone on each buil

That doesn't stop you from changing something in your working copy. The hack here is that the working copy used to build from wasn't a clean clone on each build, so just fetching changes from the (un-pwned) github repository would apply those changes and not affect the modified file on the build server.