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Most people who build e-books for a living regard Calibre as a very useful book-management tool but a rather poor publishing tool.
Much the same is true of Mobipocket Creator. It's obsolescent because it can't create a KF8 file for the Fire, Touch, etc.
As for the NCX file, I was amused to notice that the latest Kindle publishing guide--from Amazon!--nowhere mentions it. The NCX is required but not mandatory, evidently. The only thing you lose is the ability to skip from one chapter to the next (or previous), or such is the case on my K3. (I wouldn't know how to do it in the Fire.)
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