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You will want to use the mobi format. If you have the ebook in your library select mobi as the output format on the right under the red heart, select the book and click convert. You can also use the command line tool any2mobi.
As for the tale of contents, mobi doesn't really support it all that well. What will happen is the mobi conversion will parse the ebook and generate a page at the end that will be titled Table of Contents and have links to various points in the ebook. Try converting to mobi for and see how it works out.
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