The plugin depends on [[mdwn]]. If you have disabled [[mdwn]], to get [[shortcut]] work, you need commit in a shortcuts.ext (ext is `rcs|creole|html|txt|etc`), and edit/patch [[shortcut]]. Maybe use the $default_pageext is better than hardcode .mdwn?
--- shortcut.pm.orig    2009-02-12 02:05:22.000000000 -0600
+++ shortcut.pm 2009-02-12 04:41:30.000000000 -0600
@@ -23,9 +23,9 @@
        if (defined $config{srcdir}) {
                # Preprocess the shortcuts page to get all the available shortcuts
                # defined before other pages are rendered.
-               my $srcfile=srcfile("shortcuts.mdwn", 1);
+               my $srcfile=srcfile("shortcuts.$config{default_pageext}", 1);
                if (! defined $srcfile) {
-                       error(gettext("shortcut plugin will not work without a shortcuts.mdwn"));
+                       error(gettext("shortcut plugin will not work without a shortcuts.$config{default_pageext}"));
                }
                IkiWiki::preprocess("shortcuts", "shortcuts", readfile($srcfile));
        }
--[[weakish]]