Solved thanks to

https://tex.stackexchange.com/questions/671439/pandoc-from-markdown-to-pdf-how-to-restart-footnote-numbering-on-each-chapter?noredirect=1#comment1668842_671439

On Tuesday, January 10, 2023 at 10:52:54 PM UTC+1 Bastien Dumont wrote:
Pandoc, by itself, does not set the footnote numbers: in only puts \footnote{} markup in the TeX file from which the PDF is generated. So you have to search for how to do what you want in LaTeX (e.g. here: https://tex.stackexchange.com/questions/32401/footnote-backreference-with-hyperref) and to include the required commands in a custom LaTeX template or via the header-includes metadata variable.

Le Tuesday 10 January 2023 à 11:53:29AM, Javier Pastor a écrit :
> I'm trying to create several chapters for an esay I'm writing, but i'd like to
> restart footnotes numbering for each chapter and I don't know how to do it.
> After searching for information, [1]I saw this on SuperUser (StackExchange) and
> I tried to replicate the solution.
>
> In that example, the user tried to convert several .md files into an html5 one,
> but I'm trying to get a single PDF file. I generate the file, but it doesn't
> work as I wanted.
>
> The file structure is like this:
>
> chapters/
> 01-chapter.md
> 02-chapter.md
> 03-chapter.md
> format.sh
> parse.sh
>
> [2]
> parse.sh
>
> pandoc -t pdf -o ~/Documents/test.pdf --file-scope chapters/*.md
>
>
> format.sh
>
> for f in chapters/*.md;
> do
> pandoc "$f" -o "$f" -t \
> markdown+smart+footnotes-escaped_line_breaks+example_lists \
> --columns=80;
> done
>
> In this example I have the same problem as OP had:
>
> "The problem is 01-chapter.md and 02-chapter.md have both a footnote [^1].
> Basically I would like Pandoc to handle the footnotes for each file separately
> and not allow cross-referencing across my markdown files but I can't see any
> way to do this".
>
> The solution, apparently, is to use the --file-scope flag. I apply it, but on
> the resulting PDF there are two problems:
>
> 1. Footnote numbering doesn't restart: I had [1] and [2] in Chapter 1, and [1]
> and [2] in Chapter 2, but here I have [1] and [2] in Chapter 1 and [3] and
> [4] in Chapter 2.
> 2. No links back from the footnotes to the text where they were used.
>
> I'm just beginning to know pandoc and I don't understand exactly how that
> works, but I guess there must be some option in pandoc that can solve this. Any
> ideas? Thank you
>
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>
> References:
>
> [1] https://superuser.com/questions/1454255/pandoc-duplicate-footnotes-multiple-files-same-name/
> [2] https://superuser.com/posts/1454255/timeline
> [3] mailto:pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
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