Even better with
cd /media/run/usb-drive/my-backup-repo && git init --bare
Bare repositories don't have a working directory. You can still git clone / git pull from them to get the contents. You can also git push to them without clobbering any "local changes" (there aren't any).More detail here:
https://www.atlassian.com/git/tutorials/setting-up-a-reposit...