What is interesting, is that this is not the git version of magento but their public release version. So their upgrade is looking specifically for .gitignore files which normally don't exist in the production version Magento releases. Here is the output doing a diff on a fresh download from magento and your application:
As you can see, nothing differs. There is no .gitignore files on the release version of magento from their site. This may require you to submit a bug report to magento about this issue, however, I will look into it further.