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> the .git/index file, which uses mmap, is synced incorrectly by file sync tools relying on mtime

This part implies that the index file is written via mmap, but that's not true. It is fully rewritten to a new tempfile/lockfile, and then atomically renamed into place.

Git does not ever mmap with anything but PROT_READ, because not all supported platforms can do writes (in particular, the compat fallback just pread()s into a heap buffer).




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