my %with_key;
foreach my $first_key (keys %all_files) {
  foreach my $second key (keys %{$all_files{$first_key}}) {
    push @{$with_key{$second_key}}, $first_key;
  }
}

##</code><code>##

my %total;
foreach my $subhash (values %all_files) {
  foreach my $key (keys %$subhash) {
    $total{$key} += $subhash->{$key};
  }
}