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Are the system files in the folder you're tracking for the repo?
As it was 3 files I created it at command prompt (root?) level at first, then I think at some point I added all instead of the 3 files.
I moved the 3 files (.html, .css, .jpg) to a new directory and that's when the fun and games began. I've been offline this eve so can look again tomorrow maybe.
rhb
Are the system files in the folder you're tracking for the repo? If so use the the gitignore file to stop it tracking the specified files