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what if I want the repo to be added into my public_html directory?

cd to your public_html and do it there. The directory must be empty, however, or git will warn you.

On the server, I usually do one repo that is not live (a “staging” repo, as it were, for last-minute-pre-launch testing, and as a local backup), and then clone/pull the “live” site from that. You don’t have to do it that way, but I personally like it.