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#!/usr/bin/perl
use warnings; 
...

print '<?xml version="1.0" encoding="UTF-8"?>'."\n";
print $tree->as_XML();

$ perl puttyconfig.pl 
<?xml version="1.0" encoding="UTF-8"?>
<configuration savepassword="True" version="0.2.1.4">
...
  </root>
</configuration>