parse.sh

pandoc -t pdf -o ~/Documents/test.pdf --file-scope chapters/*.md

format.sh

for f in chapters/*.md;

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:

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.
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