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foreach my $file (@filenames) {
   my $h = \%files;
...

   $h->{$last} = 1;
}

foreach my $file (@filenames) {
   my $p = \\%files;
...
   $p = \(${$p}->{$_}) foreach @parts;
   ${$p} = 1;
}

foreach (@filenames) {
   my $p = \\%files;
   $p = \(${$p}->{$_}) foreach split /[-_.]/;
   ${$p} = 1;
}