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Fix git_checkout_tree() to do index filemodes correctly on Windows.
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. Conflicts: src/checkout.c
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