This is a long shot but according to the Latex user guide on Sharelatex.com, different Latex commands are used for external URLs and local files.

For further references see \href{http://www.sharelatex.com}{Something Linky} 
or go to the next url: \url{http://www.sharelatex.com} or open the next 
file \href{run:./file.txt}{File.txt}

Is pandoc capable of generating the \href{run:./file.txt}(file.txt) or is that left to Latex to figure out when PDF output is specified?

On Friday, September 15, 2017 at 10:14:01 AM UTC+10, Don Mankewich wrote:

I'm creating documents with markdown which include reference links to external PDF documents which exist in the same folder. When I use pandoc to generate a PDF document from my markdown, there appear to be links in the PDF when I hover over the labels but the external PDF does not open when I click the link. I don't get any warnings of skipped files. Here's an example of my markdown reference, it's in a numbered list.

[ats alert tables](ats-alert-database-diagram.pdf)

I have read that pandoc references relative file paths according to the directory where pandoc is executed but I'm running pandoc in the directory containing the external PDF so I shouldn't have to add further pathing information should I? I'm also using Harp JS to create a static site from my content and the link references work in Harp so I don't want to change that to support pandoc. Ideally the relative paths should for both pandoc and Harp.

Any suggestions?