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As it was said in a comment on this question -- bookdowns gitbook does not propagate things like \newcommand that work fine for the pdf_book output.

Is there a better workaround than moving the \newcommand to the first chapter's 01-intro.Rmd markdown file? This works but it somehow messes up the clean markdown syntax.

Or is there even a fix for this issue? (I didn't find anything related in the bookdown issue tracker)

Jan
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    I did some more tests (see my comment in the URL you link to). I would recommend to file a (bug/usage) report and point out that post in the issue tracker. – Marius Hofert May 05 '19 at 04:09

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