In 0.6 you can specify the --use-auto-toc option. "Force use of auto-generated Table of Contents" in the GUI. If it is still having trouble finding the chapters you can specify the xpath for it to identify them. E.G. --level1-toc=//*[((name()='h1' or name()='h2') and re:test(., 'chapter|book|section|part\s+', 'i')) or @class = 'chapter']. "Detect Chapters" in the GUI.
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