This blogpost is of the kind: I don't want to forget that this exists, therefore I hope it helps you, but it's mine. :o)
Magento updates are pain, because of the damn fcking cockspl*t @copyright header.
Thanks to Franklin P Strube there is a solution for this:
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Copy your new magento version over the old one.
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Run the command:
git diff -G '@copyright.*[Cc]opyright' --name-only | xargs -I {} sh -c 'FILE={} ; [ $(git diff -U0 -- $FILE | wc -l | tr -d " " | cut -f1-) -eq 7 ] && git add $FILE'
Then most of the files which contain the copyright header are staged. Unforunately when I'm reading the command correctly, the whole file is staged, not only the line. Maybe only the files are added where ONLY the copyright header is changed. Please try.
There is a second answer from Luke H which might help too. I don't understand a word of these commands, so no description.