[1] => StringA
[2] => StringB
...
[A] => [1, 2]
[B] => [2]
[download]

[A]    => [1]
[A, B] => [2]
[download]

Where do StringA, StringB etc. come from? If they are in files, couldn't you store the file paths rather than their values?

[1] => '/path/to/StringA/data'
[2] => '/path/to/StringB/data'
[download]

Here is my attempt:

use strict;
use warnings;
use Data::Dumper;

my @data = 
    map { [ [split /,\s*/, $_->[0]],  [split /,\s*/, $_->[1]] ] }
    map { /\[(.*)\]\s*=>\s*\[(.*)\]/ ? [ $1, $2 ] : () } <DATA>;

my %inverted;
for my $d (@data) {
    undef @{$inverted{$_}}{@{$d->[0]}} for @{$d->[1]};
}

my %invertagain;
push @{ $invertagain{join ",", sort keys %{$inverted{$_}}} }, $_ for k
+eys %inverted;

print Dumper \%invertagain;
__DATA__
[a, b, c] => [1, 2, 3]
[b, c]    => [2, 3, 4, 5]
[a, c, d] => [4, 5, 6, 7]
[d]       => [1, 2, 6]
[download]

"if you take a closer look" to what you said:

> the result should look like this:¹

[a, b, c, d] => [1, 2] 
[b, c] => [2]
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which doesn't make sense, don't you agree?

You are talking about a "hashtree" but the data shown has nothing to do with HoH.

The data shown isn't even valid Perl, keys are strings never arrays.

have a look at How (Not) To Ask A Question

Asking a good question is often the best answer! :)

Cheers Rolf

( addicted to the Perl Programming Language)

¹) OP updated now...

first you are right.. i made the result manually.. that was a simple mistake.. :)

actually it is an hash tree.. but i dont want to deflect the problem with code snippets..

keys are strings never arrays
[download]

i dont agree.. just take a look at Hash::Multikey or perldsc or maybe it is a nested structure like this:

#!/usr/bin/perl -w
use strict;
use warnings;

my %hash;
$hash{'number'}{'even'} = [24, 44, 38, 36];
$hash{'number'}{'odd'} = [23, 43, 37, 35];

foreach my $i(keys %hash){
    print $i;
    foreach my $j(keys %{$hash{$i}}){
        print "\t".$j."\t";
        print join(" ",@{$hash{'number'}{$j}})."\n";
    }
}
[download]

furthermore thats offtopic :)
$perlig =~ s/pec/cep/g if 'errors expected';