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

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

foreach $filepath (get_file_list($dir)) 
{
...
            ...
        }
    );

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

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