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git_checkout_index can now check out other git_index's (that are not
necessarily the repository index). This allows checkout_index to use
the repository's index for stat cache information instead of the index
data being checked out. git_merge and friends now check out their
indexes directly instead of trying to blend it into the running index.
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There were a couple of "init_opts()" functions a few more cases
of structure initialization that I somehow missed.
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We treat this as a NUL-terminated string, so make sure that we add the
terminator.
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