Without having reread the relevant FAQ entry: You'd have to provide a contents.html as part of the HTML format of the ebook and add all the chapters as well. Adding every HTML file as a separate book will not help you in any way. The format of the contents.html is given in the FAQ entry, if you have any trouble, I can post a script I hacked together once that sort of throws a content.html together, although with no regard to sorting. You could hack it further, if it would help.
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