include-in-header overwrites header-includes

[tolot27]

With pandoc v2.1.1 -H/--include-in-header overwrites header-includes: provided in the yaml block of the input markdown. According to the manual, it should Include contents of FILE, verbatim, at the end of the header.

Example file header_with.md with content:

---
title: metatest
author: Mathias Walter
header-includes:
  - '`\usepackage{todonotes}`{=latex}'
...

# Test

Some text.

additional.tex:

\usepackage{multicol}

Command: pandoc -s -t latex header_with.md -H additional.tex

The line \usepackage{todonotes} does not appear in the output anymore:

\PassOptionsToPackage{unicode=true}{hyperref} % options for packages loaded elsewhere
\PassOptionsToPackage{hyphens}{url}
%
\documentclass[]{article}
\usepackage{lmodern}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[T1]{fontenc}
  \usepackage[utf8]{inputenc}
  \usepackage{textcomp} % provides euro and other symbols
\else % if luatex or xelatex
  \usepackage{unicode-math}
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage[]{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
\usepackage{hyperref}
\hypersetup{
            pdftitle={metatest},
            pdfauthor={Mathias Walter},
            pdfborder={0 0 0},
            breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{0}
% Redefines (sub)paragraphs to behave more like sections
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi

% set default figure placement to htbp
\makeatletter
\def\fps@figure{htbp}
\makeatother

\usepackage{multicol}

\title{metatest}
\author{Mathias Walter}
\date{}

\begin{document}
\maketitle

\hypertarget{test}{%
\section{Test}\label{test}}

Some text.

\end{document}

[jgm]

Dup of #3139? See the discussion there.

[tolot27]

Closing in favor of #3139 and continue at pandoc-discuss.
Nevertheless, the documentation is incorrect because the "contents of FILE" is not really included at the end of the header because it replaces some part.

[jgm]

the documentation is incorrect because the "contents of FILE" is not really included at the end of the header because it replaces some part.

The FILE in this case is additional.tex (that's the argument to -H). It is included in full:

\usepackage{multicol}

[tolot27]

included at the end of the header

That part is wrong because it is not included at the end rather than it replaces the complete header-include part.