"Spine file" is a good way to think of it. It's an XML file that contains all the metadata for the ebook as well as a manifest of of the component html file(s), optional cover image, etc.
My main ebook creation tool right now is MobiCreator. I like it for a bunch of reasons, one of which is that it makes an OPF file as an intermediate step. After making the Mobi ebook, I then use the OPF file with html2epub to make the epub version.
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