When applying to both the index and the working directory, ensure that
the index contents match the working directory.  This mirrors the
requirement in `git apply --index`.

This also means that - along with the prior commit that uses the working
directory contents as the checkout baseline - we no longer expect
conflicts during checkout.  So remove the special-case error handling
for checkout conflicts.  (Any checkout conflict now would be because the
file was actually modified between the start of patch application and
the checkout.)