Since the verification file is within the web servers root structure, and Google needs to access it to read its contents - Technically anyone could read it if they wanted by going to http://mysite.example.com/verification.html.
With that in mind, I wouldn't add it to the github repository as it isn't something anyone would need to either clone the repository and create their own version, or fork and create change requests. It doesn't have any value to anyone other than you.