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Why isn't anybody understanding?
Calibre takes the NCX and generates a ToC from it for the Mobi. It is put at the back. Yes it's HTML and not NCX. I didn't say otherwise. And yes it is guide linked. What it isn't is near the front of the eBook.
Mobipocket Reader doesn't deal with the NCX file properly when t converts an ePub. I'm guessing Kindlegen botches the ToC as well.
I blame publishers for kow-towing to Amazon. Because if not for Amazon's botched conversion software, there would be no need for an internal ToC in an ePub.
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