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I'm a bit unclear. Is your markdown being converted properly. Is the issue of it not detecting chapters because it's not converting the markdown markup into the appropriate heading types? Or is the conversion coming out looking correct but just missing the chapters in the TOC?
Awhile back the TXT input was changed to auto detect the formatting (Markdown, Textile). If it's converting and you are seeing the ##chapters coming though as headings then auto detection is working properly. The only time you need to use "--formatting-type markdown" is when auto detection fails and you need to force the use of markdown.
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