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Neither Calibre nor Kindlegen create an inline TOC from the NCX TOC. They will incorporate the NCX data into the MOBI file so that it's there for the ereader device or app to make use of, e.g. on the Kindle, navigation point markers are placed on the progress bar, corresponding with the navigation points coded into the NCX file, and the 5-way control button can be used to skip to the previous or next navigation point.
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