I'm a little stumped as to the funky matching that goes on when sub handleABC is embedded in the substitution. Within the function, my @c = split /\[%\s+ELSE\s+%\]/s, $b, 2; splits yoda [% ELSE %] JEFFA correctly into "yoda " and "jeffa ", while within the substitution, it gets split into "" and "yoda [% ELSE %] JEFFA".

I tried searching for threads on this but they're kind of hard to find.
P.S. If you're worried about wheels and such (you shouldn't), a bug in CGI::Kwiki spawned this. 

use strict;
use warnings;
use constant DEBUG => @ARGV;

my $v = { stuff => 0 };

my $template = '[% IF stuff %] yoda [% ELSE %] JEFFA [% END %]';

my $ot = $template;

    $template =~ s{
        \[% \s+ IF \s+ (\w+) \s+ %\] # $1 var
        (.*?)                        # $2 then    
        \[% \s+ END \s+ %\]
    }
    [
        my( $a, $b, $c ) = ($1, $2, '');
#        handleABC($v, $a,$b,$c);

        if($b =~ m/\[% \s+ ELSE \s+ %\]/gsx ){
            my @c = split /\[%\s+ELSE\s+%\]/s, $b, 2;
            warn "c(",join('|',@c),")" if DEBUG;
            $b = $c[0];
            $c = $c[1];
        }

       warn "a($a) b($b) c($c)\n----\n" if DEBUG;

        defined $v->{$a} && $v->{$a} ? $b : $c;

    ]gsex;

warn " \n\n ------------------ \n\n" if DEBUG;

$ot =~ s{
        \[% \s+ IF \s+ (\w+) \s+ %\] # $1 var
        (.*?)                        # $2 then    
        \[% \s+ END \s+ %\]
    }
    [
        handleABC($v, $1, $2, '');
    ]gsex;

print ">>>$template<<<\n";
print ">>>|$ot|<<<\n";

sub handleABC{
    my( $v, $a, $b, $c ) = @_;

        warn "----\na($a) b($b) c($c)" if DEBUG;

        if($b =~ m/\[%\s+ELSE\s+%\]/s ){
            my @c = split /\[%\s+ELSE\s+%\]/s, $b, 2;
            warn "c(",join('|',@c),")" if DEBUG;
            $b = $c[0];
            $c = $c[1];
        }

       warn "a($a) b($b) c($c)\n----\n" if DEBUG;

        defined $v->{$a} && $v->{$a} ? $b : $c;
}
__END__
>>>yoda [% ELSE %] JEFFA <<<
>>>| JEFFA |<<<

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In reply to matching / splitting within a substitution by PodMaster

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