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1. That is a suggestion, not a requirement. In 0.6 calibre leaves the organisation of html file up to the user. If the user puts them in sub dirs, they will be in sub dirs in the generated EPUB
2. This is likely a bug in okular
3. Be more specific. Chapter recognition works fine for me. Rememebr that the XPath syntax has changed. You now have to prepend h: to all HTML tag names
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