setup.cmd should make pre-commit hooks executable

[rjyounes]

At least on Mac, when setup.cmd runs and copies the pre-commit hook into ./git/hooks, it needs to be made executable - after the copy. If there isn't already an executable file in the hooks directory, it gets copied as non-executable, regardless of the status of the original file in tools.

We should also make the pre-commit in the serializer executable, in case it hasn't come in that way from the repo.