Strictly speaking, changing the permissions *is* a change. If you want your local change recorded then... (from the root of your Moodle install)
git add .
git commit -m 'changing file permissions'
gets you to the same place, and the change is now logged in your git history. If you care.
When I tried this, it seemed to want me to add all of the untracked files as well. I have a bunch of untracked files that I didn't care to have tracked just yet, so for the sake of expedience, I just toggled the core.filemode option instead of fussing with ignore lists. I wouldn't mind fixing this more completely some day, but I didn't want a simple update spiraling into a much longer escapade.
While I understand now that changing permissions counts as a file change where Git is concerned, I still think it might be useful to indicate that somewhere in the documentation. I'm willing to help with that, if help is needed.
