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Adding a table of contents isn't a trivial operation, given the lack of programs for editing mobi files. For ePubs, you can use Sigil, an excellent ePub editor. Even with Sigil, the TOC must be added manually, as I understand it (I've only used it for other things). Calibre can add a TOC to a book, but you have to know how to use regular expressions (regex). And even that will not reliably work on many books.

Neither Sigil or Calibre will do any TOC operations to a DRM protected book. Basically, it's up to the publisher.

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