make in Cygwin stomps files in .git/hooks/

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Hi,

I'm on Windows using Cygwin to build LibreOffice. When I "make", the files in .git/hooks/
  commit-msg  post-merge  pre-commit  README
are overwritten with 0 byte files. This causes "git commit" (using SourceTree) to fail: "Commit: cannot spawn .git/hooks/pre-commit: No such file or directory." Launching cygwin.bat as admin doesn't help.

Any ideas how I can fix this?

Thanks,
Marc

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