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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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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>

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