The solution to this is actually quite simple. The values in a hash must be scalars. References are scalars. So use array references as the hash values.

Replace

      $href{$1} = $2 if $_ =~ /(\S+)\s+(\S+)/;
[download]

with

      push @{$href{$1}}, $2 if $_ =~ /(\S+)\s+(\S+)/;
[download]

You'll need a little more work to use the value data, but you haven't lost any of it.

   while (my ($key, $value) = each(%href)) {
          print "$key, (@{$value})\n";
   }
[download]

The rest of your code will need similar modifications to adapt to arrays of values.