I'm always surprised when I produce a PDF with pandoc via context output and the hyperlinks are indistinguishable from normal text so I can't tell where they are. It turns out that the template for context output unconditionally sets linkstyle, linkcolor, and contrastcolor to the values of the variables $linkstyle$, $linkcolor$, and $linkcontrastcolor$
even if the user hasn't specified them. This forces those all off.
Here's the code from pandoc -D context (pandoc version 2.14.0.1):
% Enable hyperlinks
\setupinteraction
[state=start,
$if(title)$
title={$title$},
$endif$
$if(subtitle)$
subtitle={$subtitle$},
$endif$
$if(author)$
author={$for(author)$$author$$sep$; $endfor$},
$endif$
$if(keywords)$
keyword={$for(keywords)$$keywords$$sep$; $endfor$},
$endif$
style=$linkstyle$,
color=$linkcolor$,
contrastcolor=$linkcontrastcolor$]
I think the last three lines should be
contrastcolor=$linkcontrastcolor$
instead, so the style, color, and contrast color are only set if the user specifies those variables. This way the document gets the default ConTeXt style, color, and contrast color.
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