git_checkout_tree() has some fallback behaviors for file systems
which don't have full support of filemodes.  Generally works fine,
but if a given file had a change of type from a 0644 to 0755 (i.e.,
you add executable permissions), the fallback behavior incorrectly
triggers when writing hte updated index.

This would cause a git_checkout_tree() command, even with the
GIT_CHECKOUT_FORCE option set, to leave a dirty index on Windows.

Also added checks to an existing test to catch this case.