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The standalone 'markdown' utility is perfectly happy with an external link inside a <h1>, e.g.:

# Review of [Dwarf Fortress][]
...
[Dwarf Fortress]: http://www.bay12games.com/dwarves/

produces

<h1>Review of <a href="http://www.bay12games.com/dwarves/">Dwarf Fortress</a></h1>

but when I try to use this construct in an ikiwiki page, I get

<h1>Review of [Dwarf Fortress][]</h1>

It works fine with h2 and deeper. The square brackets also appear in the output of an [[directive/inline]] directive in archive mode, I haven't tried non-archive mode.