my @variable;
for (... )  {
   ...
   undef @variable;
}

##</code><code>##

for (...) {
    my @variable;
    ...
    # no manual cleanup necessary.
}

##</code><code>##

foreach $filepath (get_file_list($dir)) 
{
    my (%company_hist, @company_list, %reference_hist, @reference_list) ;
    my $twig = XML::Twig -> new(
        twig_roots => {
            company  => sub { push @company_list, $_[1]->{'att'}->{'code'} },
            ...
        }
    );

##</code><code>##

#my($k, $v);
#while ( ($k,$v) = each %reference_hist ) {
#print "$k => $v\n";
#}

##</code><code>##

use Data::Dumper;
...
print Dumper \%reference_hist;