You want to back up the /home/mywebsite/public_html and MySQL files on the server. If your content is static then you don't need to back it up. But if your running MySQL then I would back it up daily. I back my server up two ways. First I back up the files on the server to the backup hard drive. Then I download the files to my workstation. And once a month I burn them to CD. So I have 3 backup copies should anything happen.
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