Given $file_hash, $dir and $file_name, do the insertion like this:

push @{ $file_hash->{$dir} }, $file_name;

The arrays that $file_name are pushed into will be created automagically by Perl.

Then to create the report:

foreach my $file_dir (sort keys %{$file_hash})
{
  foreach my $file (@{ $file_hash->{$file_dir} }){
        print "$counter Directory: $file_dir $file\n";
        $counter++;
  }
}
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