I guess you could think of it this way: My goal was to combine functionality from the 3 different filters in the way I described, since no filter exists which can do all of those things in one go.  My first attempt at achieving that goal was very crude, since I sequentially applied the three filters and expected them to be compatible with each other. I ran into the compilation error at that point, which is why I started this thread. Upon further discussion/thought, I started to realize that even if I do fix the compilation error (which is a LaTeX problem), that doesn't guarantee that the functionality will be combined in the way I expect (which is a pandoc/Lua/AST problem).

On Tue, 7 Mar 2023 at 20:19, <bastien.dumont@posteo.net> wrote:
Recalling your original post:

> I get an error upon compilation, because pandoc-crossref defines its own
> header include which gets overwritten by my -H header.tex.

Do you mean now that you resolved this problem and ran into another one?
They are distinct issues, even if they affect you simultaneously, aren't they?

Le Tuesday 07 March 2023 à 07:28:26PM, A A a écrit :
> I’m already familiar with pandoc templates, but I don’t think they are the
> solution here. You might recall I’m using 3 distinct filters, namely
> pandoc-crossref.lua, minted.lua, include-code-files.lua. I’m using each because
> of some functionality it provides:
>
>   • pandoc-crossref.lua: The ability to cross-reference listings and caption
>     them
>   • minted.lua: The ability to break long code lines within a listing.
>   • include-code-files.lua: The ability to include external files in a listing.
>
> I expected that using these filters in unison would result in an intersection
> of the mentioned functionality. However, this is incorrect. The underlying
> issue here is that they all act on the same AST element (i.e. CodeBlock) and
> calling them sequentially like that will inevitably result in conflicts.
>
> As you can see it doesn’t really matter what I do with the template or the
> header, because neither of those two things act on the AST.
>
>
> On Tue, 7 Mar 2023 at 16:51, Bastien DUMONT <[1]bastien.dumont-VwIFZPTo/vqsTnJN9+BGXg@public.gmane.org>
> wrote:
>
>     You can get the default template for LaTeX with pandoc -D latex, customize
>     it according to your needs and specify the resulting file with --template
>     in the command. There is nothing specific here for pandoc-crossrefs. See
>     the section about templates in the manual of Pandoc for more details.
>
>     Le Tuesday 07 March 2023 à 02:06:17PM, A A a écrit :
>     >     You can include it in an external metadata file referred to via the
>     >     —metadata-file option
>     >
>     > I believe that would still be a YAML file with weird syntax like this?
>     >
>     > header-includes:
>     > - |
>     >   ~~~{=latex}
>     >   \let\oldsection\section
>     >   \renewcommand{\section}[1]{\clearpage\oldsection{#1}}
>     >   ~~~
>     >
>     > If so then yes, I definitely prefer doing my own header.tex. But this
>     would
>     > have to include all the content necessary for pandoc-crossref to work
>     properly.
>     > Any ideas where I could find this content? I briefly skimmed the
>     > pandoc-crossref repo but didn’t find anything obvious…
>     >
>     >
>     > On Tue, 7 Mar 2023 at 12:16, Bastien DUMONT <[1][2]
>     bastien.dumont-VwIFZPTo/vqsTnJN9+BGXg@public.gmane.org>
>     > wrote:
>     >
>     >     You can include it in an external metadata file referred to via the
>     >     --metadata-file option. However, if you customize the LaTeX preamble
>     >     heavily, it may be preferable to use a custom template including the
>     >     content of header.tex.
>     >
>     >     Le Tuesday 07 March 2023 à 12:07:19PM, A A a écrit :
>     >     > That would force me to put my header content within my markdown
>     file and
>     >     remove
>     >     > "header.tex" completely. I would very much prefer to keep them as
>     >     separate
>     >     > files. 
>     >     >
>     >     > The header.tex for my use case ia much more involved. Including it
>     inside
>     >     the
>     >     > markdowm YAML block like that would be quite ugly IMO.
>     >     >
>     >     >
>     >     >
>     >     >
>     >     >
>     >     > On Tue, 7 Mar 2023, 10:16 Bastien DUMONT, <[1][2]
>     >     [3]bastien.dumont-VwIFZPTo/vqsTnJN9+BGXg@public.gmane.org> wrote:
>     >     >
>     >     >     Since you don't use a custom template, you don't have to add
>     $for
>     >     >     (header-includes)$ etc. anywhere: it is already included in the
>     >     default
>     >     >     LaTeX template.
>     >     >     The answer for your use case is here: [2][3][4]https://
>     github.com/
>     >     lierdakil/
>     >     >     pandoc-crossref/issues/47#issuecomment-614404532
>     >     >
>     >     >     Le Tuesday 07 March 2023 à 10:02:38AM, A A a écrit :
>     >     >     > Files
>     >     >     >
>     >     >     > test.py
>     >     >     >
>     >     >     > def f(x):
>     >     >     >     return x
>     >     >     >
>     >     >     > test.md
>     >     >     >
>     >     >     > ~~~{
>     >     >     >   #lst:test
>     >     >     >   .py
>     >     >     >   include="test.py"
>     >     >     >   caption=`test.py`
>     >     >     > }
>     >     >     > ~~~
>     >     >     >
>     >     >     > header.tex
>     >     >     >
>     >     >     > \usepackage{minted}
>     >     >     >
>     >     >     > \definecolor{bg}{rgb}{0.85, 0.85. 0.85}
>     >     >     > \setminted{breaklines=true, bgcolor=bg, breakanywhere}
>     >     >     >
>     >     >     > Compilation
>     >     >     >
>     >     >     > I’m compiling with:
>     >     >     >
>     >     >     > pandoc -s -F pandoc-crossref -L include-code-files.lua -L
>     >     minted.lua -H
>     >     >     header.tex --from markdown --to latex test.md -o test.tex
>     >     >     > latexmk --shell-escape -pdflatex test.tex
>     >     >     >
>     >     >     > I get an error upon compilation, because pandoc-crossref
>     defines
>     >     its own
>     >     >     header
>     >     >     > include which gets overwritten by my -H header.tex. This [1]
>     link
>     >     provides
>     >     >     more
>     >     >     > information.
>     >     >     >
>     >     >     > I tried the solution proposed by @lierdakil in the link
>     provided
>     >     but get
>     >     >     an
>     >     >     > error:
>     >     >     >
>     >     >     >     ! LaTeX Error: Missing \begin{document}.
>     >     >     >
>     >     >     >     See the LaTeX manual or LaTeX Companion for explanation.
>     >     >     >     Type H for immediate help.
>     >     >     >
>     >     >     >     l.97 $
>     >     >     >     for(header-includes)$
>     >     >     >     ?
>     >     >     >
>     >     >     > So I’m at a bit of a loss regarding what to do here, Any
>     pointers
>     >     >     welcome.
>     >     >     > Thanks
>     >     >     >
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>     >     >     > [1] [6][7][8]https://github.com/lierdakil/pandoc-crossref/
>     issues/47
>     >     >     > [2] mailto:[7][8][9]
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>     >     issuecomment-614404532
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>     > [2] mailto:[37]bastien.dumont-VwIFZPTo/vqsTnJN9+BGXg@public.gmane.org
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>     > [6] [41]http://40mail.gmail.com/
>     > [7] [42]https://github.com/lierdakil/pandoc-crossref/issues/47
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>     > [17] [52]https://github.com/lierdakil/pandoc-crossref/issues/47#
>     issuecomment-614404532
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> [6] http://groups.google.com/
> [7] http://40mail.gmail.com/
> [8] https://github.com/lierdakil/pandoc-crossref/issues/47
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