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  my %h;
  for my $file ( glob "*.[abc]" )
...
      push @{ $h{$file_k0}{$file_k1} }, [ split /\t/ ];
    }
  }

  for my $file_k0 ( sort keys %h ) {
    for my $file_k1 ( sort keys %{ $h{$file_k0} } ) {
...
      }
    }
  }