#!/usr/bin/perl

use strict;
use warnings;

use File::Find::Rule;
use XML::LibXML;

# get a list of target files
my $input_folder = 'input'; # whatever
my @files = File::Find::Rule->file->in( $input_folder );

# initiate XML parser
my $parser = XML::LibXML->new;
$parser->expand_entities( 0 ); # leave entities alone

# go through target files, collecting elements of interest
my @wanted;

foreach my $file ( @files ) {

	# parse XML
	my $dom = $parser->parse_file( $file ); # input

	# select and store all top level elements
	push @wanted, $dom->documentElement->findnodes( './*' ); 
}

# make a new document
my $new = XML::LibXML::Document->new( '1.0', 'UTF-8' );

# add root element
my $root = XML::LibXML::Element->new( 'xml' );
$new->addChild( $root );

# add the inner elements we've collected
$root->addChild( $_ ) for @wanted;

# output
print $new->toString;