Using XML::LibXML you can do (assuming you've put the XML in test.xml):

#!/usr/bin/env perl

use strict;
use warnings;
use XML::LibXML;


my $doc =  XML::LibXML->new()->parse_file('test.xml');
my $new_parent = ($doc->findnodes('//module [@name="all"]'))[0];
my @nodes = map {$_->getAttribute('name')} $doc->findnodes('//module [
+@name="all"]/moduleref');

my ($old_node, $new_node);
foreach (@nodes) {
    $old_node = ($doc->findnodes('//moduleref [@name="' . $_ .'"]') )[
+0];
    $new_node = ($doc->findnodes('//module [@name="'.$_ .'"]'))[0];
    next unless $new_node;
    $old_node = $new_parent->replaceChild($new_node, $old_node);
}       
print $doc->toString;
[download]