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Fix git_repository_set_index() refcount issue
git_repository_free() calls git_index_free() if the owned index is not null. According to the doc, when setting a new index through git_repository_set_index() the caller has still to take care of releasing the index by itself. In order to cope with this, this fix makes sure the index refcount is incremented when a new repository is being plugged a new index.
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