Pandoc supports a YAML metadata block in markdown documents. This can set the title and author, etc. It can also manipulate the appearance of the PDF output by changing the
YAML metadata are not passed to pandoc as arguments, but as variables. When you call pandoc on your MWE, it does not produce this :
pandoc -o guide.pdf articheck_guide.md --toc --number-sections
as we think it would. rather, it calls :
pandoc -o guide.pdf articheck_guide.md -V toc:yes -V number-sections:yes
Why, then, does you MWE produces a toc? Because the default latex template makes use of a toc variable :
~$ pandoc -D latex | grep toc
$if(toc)$
\setcounter{tocdepth}{$toc-depth$}
So setting toc to any value should produce a table of contents, at least in latex output. In this template, there is no number-sections variables, so this one doesn't work. However, there is a numbersections variable :
~$ pandoc -D latex | grep number
$if(numbersections)$
Setting numbersections to any value will produce numbering in a latex output with the default template
---
title: My Title
toc: yes
numbersections: yes
---
The trouble with this solution is that it only works with some output format. I thought I had read somewhere on the pandoc mailing-list that we soon would be able to use metadata in YAML blocks as intended (ie. as arguments rather than variables), but I can't find it anymore, so maybe it won't happen very soon.