Goodness gracious me!  It's all worked out.  I started using `-H` for including the tex files some years ago not to avoid using `header-includes`, but because I couldn't get in-file `headers-include` to work properly.  It probably wasn't working correctly back then because I hadn't used ```{=latex}.  But now, finally, this worked, when placed in the in-file YAML metadata block:
```
header-includes: |
  ```{=latex}
  \usepackage{microtype,parskip,bookmark,setspace,xurl,secdot}
  \setlength{\parskip}{9pt plus1pt}
  \setlength{\parindent}{1.5em}
  \usepackage[hang,bottom,multiple]{footmisc}
  \setlength{\footnotesep}{3mm}
  ```
```

Thanks so much John!

I think eventually I will try to learn a bit of Lua to write a filter for this, since it's a bit ungainly to keep copy-pasting this snippet into each document I write.

One work-around (I think, if that's the right word), which seems to work for me:

Create a latex-headers.md with the above `header-includes` YAML metadata, and include it as an input file (from being "markdown") in addition to your main file.  Then it seems to (a) get parsed as markdown, (b) recognized as `headers-includes` metadata, (c) results in the LaTeX being used to create PDFs, but not showing up in the HTML.

And thank you so much for the defaults system. It's a game-changer for the coding-challenged amongst us.
On Wednesday, 26 August, 2020 at 11:49:07 am UTC+5:30 John MacFarlane wrote:

OK, I thought you were talking about metadata in the document,
not defaults.yaml. defaults.yaml isn't quite the same -- it
is a way of specifying default values for things you can specify
on the command line, and they work the same for the most part.
Metadata in defaults.yaml files is NOT parsed as Markdown,
but rather as plain text, just like --metadata on the command line.

This is pointed out in the documentation, which notes:

# metadata values specified here are parsed as literal
# string text, not markdown

If you want to include some metadata conditionally,
depending on the output format, but NOT by adding
header-includes to the YAML metadata in a markdown
file, then your best bet is to use a lua filter, which
has access to the output format in the FORMAT variable
and can insert the appropriate thing into header-includes
in the document's metadata.


Pranesh Prakash <the.so...@gmail.com> writes:

> On Wednesday, 26 August, 2020 at 3:14:37 am UTC+5:30 John MacFarlane wrote:
>> header-includes is the field name to use.
>
> If I use header-includes in my defaults.yaml file thusly, without
> back-ticks:
> ---
> metadata:
> header-includes: |
> \usepackage{microtype,parskip,bookmark,setspace,xurl,secdot}
> \usepackage[hang,bottom]{footmisc}
> \setlength{\footnotesep}{3mm}
> ...
>
> I get the following error:
>
>> Error producing PDF.
>> ! LaTeX Error: Missing \begin{document}.
>>
>> See the LaTeX manual or LaTeX Companion for explanation.
>> Type H <return> for immediate help.
>> ...
>>
>> l.43 \textbackslash
>
> If I use header-includes in my defaults.yaml file thusly, with back-ticks:
> ---
> metadata:
> header-includes:
> - |
> ```{=latex}
> \usepackage{microtype,parskip,bookmark,setspace,xurl,secdot}
> \usepackage[hang,bottom]{footmisc}
> \setlength{\footnotesep}{3mm}
> ```
> ...
>
> I get the following error:
>
>> Error producing PDF.
>> ! LaTeX Error: Missing \begin{document}.
>>
>> See the LaTeX manual or LaTeX Companion for explanation.
>> Type H <return> for immediate help.
>> ...
>>
>> l.43 `
>
> Regards,
> Pranesh
>
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