Issues with using include-before/include-after when output is pdf

[Tahir B <tahir.butt-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>]

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I wanted to format the body of my article text such that paragraphs (all 
but first in a section) were indented and that lines were spaced out. But I 
wanted the bibliography to not be indented and have normal spacing.

Following the instructions I got from some Google searches I thought the 
following would do the trick:

---

title: This is a test
linestretch: 1.5
header-includes:
    - \usepackage{fullpage}
include-before:
    - \setlength{\parindent}{15pt}
include-after:
    - \setlength{\parindent}{0pt}
    - \setstretch{1}

---


Unfortunately this did not work as I had hoped. I tried three approaches for generating a pdf: just pandoc, pandoc+csl+latex, pandoc+biblatex+latex. In all three cases what I found was that the include-after lines were added actually after the bibliography command had been called.


Here is my attempt to reproduce the issue: 


https://gist.github.com/majorgreys/af344eb9824b947f393b


In the pandoc+csl+latex outputted tex file I got this:


\section*{References}\label{references}
\addcontentsline{toc}{section}{References}

Last, First. 1981. \emph{Book Title}. Publisher.

---------. 2001. \emph{Book Title 2}. Publisher.

\setlength{\parindent}{0pt}

\setstretch{1}


And, in the pandoc+biblatex+latex outputted tex file I got this:


\printbibliography[title=References]

\setlength{\parindent}{0pt}

\setstretch{1}


This then led me to look at the default latex template, where the relevant lines are:


$body$

$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}

$endif$
$endif$
$if(biblatex)$
\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$

$endif$
$for(include-after)$
$include-after$

$endfor$


Now it makes sense why in all three approaches the include-after clauses do not end up affecting the bibliography.


I can certainly modify the latex template so that the include-after block is before the natbib block. But that only resolves the issue when I'm not using citeproc.


I wonder if include-after behavior for straight pdf output should actually be like the modified latex template I just described. Should $body have the citeproc-generated bibliography appended to it or should the include-after applied before the bibliography is inserted into the document? I expected that the latter would be how things worked, but maybe there are many good reasons for the former to be the typical behavior.


Hope my issue and questions made sense.


Thanks!

Tahir

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