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Unlike other format, ikiwiki is somehow depends
on mdwn, since the underlay dir
is written in mdwn. If you want to disable mdwn,
you need to overwrite the underlay
dir (set underlaydir in ikiwiki.setup
to your own underlay dir or replace underlay pages
in your $SRC).
Specially, the [[shortcut]] plugin is hardcoded to
use shortcuts.mdwn. So you need pay more care if
you [[use shortcut without mdwn|shortcut/discussion]].
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