How do I remove files saying “old mode 100755 new mode 100644” from unstaged changes in Git?

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That looks like unix file permissions modes to me (755=rwxr-xr-x, 644=rw-r--r--) – the old mode included the +x (executable) flag, the new mode doesn’t.

This msysgit issue’s replies suggests setting core.filemode to false in order to get rid of the issue:

git config core.filemode false

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