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You have to use the :minlevel option on the #+INCLUDE: line to get to start at the second level (the corollary is that you might as well not worry about the levels in itself): #+INCLUDE: #+INCLUDE: :minlevel 2 * I have another second level section ... but that is set through the #+INCLUDE directive in the ...


There is no obvious link with elpy package in your settings. Two small modifications of your code seems to be needed: In your org file you need: #+BEGIN_SRC sh only. In your init file, you need to add: (require 'ob-sh) to org configuration. Then the html file is generated without problems. I suggest also to upgrade to org 9.x

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