Suppose the user wants to set a new cover in an epub file. Now should calibre replace the first entry in the spine or not? That is the question.
The only way to unambiguously answer it is to have some pointer in the OPF file that tells calibre whether the first entry in the spine is a cover or not.
Try to guess if the first entry is a cover is not at all robust, just take my word for it, I lack the patience to enumerate all the cases where any guessing algorithm will fail.
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