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i've just installed Pandoc on Kubuntu 14.04 and envision using it on a sort of homebrew markdown.txt files that will be used as chapters in a book (using koma script scrbook). The book already has a master file and preamble. I'd just like to somehow customize Pandoc to convert my own format, a sort of markdown.

Was pandoc designed for that (customization) or can only export it to a report like document with computer modern fonts? If so, how do I tell pandoc to not define a class etc, since my preamble does all that.

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Pandoc defines the preamble etc only if you set the standalone option '-s'. Leave it out and you are good to go.

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