Looks like they weren't staged. He clicked on the staging option, it showed it would stage thousands of files, he said "hey I should fix my .gitignore" and clicked on what looked like either a "don't stage" or a "forget" button, and it was a "checkout --force" button.

The most impressive thing is all the people doubling down on the idea that a "checkout --force" button in a main interaction screen is a great idea, there's nothing wrong with the software, and the user is a moron.