<d1b2>
<hansemro> So to elaborate, the site cannot number chapters and can only number sections within each chapter without chapter number prefix (chapter 3. section 1. -> 1.). The PDF output, on the other hand, does number chapters and prefixes each section with the appropriate chapter number (chapter 3. section 1. -> 3.1.).
<d1b2>
<hansemro> As for figures, the figure index resets to 1 for each chapter in the site version, but increments by 1 without resetting in the PDF.