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


1

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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