How to patch a file that is not in a module's git repo?
That gihub repository looks to be outdated, as the last commit was made May 15, 2020
To see a module's repository, go to the projects page and click on on &quot;Browse code repository&quot;

Which will take you to the GitLab repository.


So where is this directory?

Well... that directory doesn't exist. Maybe your composer.json already contains a patch that creates it? OR someone manually added that folder and file, as that folder and file is not officially part of Commerce.