solution for 5

deps

A: B
B: C, D
E: D

deps.pl

use strict;
use warnings;

use v5.14;

my %deps;

# A line looks like this:
# module: dep1, dep2, dep3
#
# We add it to the hash as an array ref
# A: B
# B: C, D
# C: D
sub insert_line_to_hash {
    my ($line) = @_;

    my ( $module, $deps ) = split /\s*:\s*/, $line;
    my ( @deps ) = split /\s*,\s*/, $deps;

    $deps{$module} = \@deps;
    foreach my $m (@deps) {
        if ( ! exists $deps{$m}   ) {
            $deps{$m} = [];
        }
    }
}

sub get_next_product {
    my $result;

    while ( my ($k, $v ) = each %deps ) {
        # found it
        if ( @$v == 0 ) {
            $result = $k;
        }
    }
    # returns false
    return $result;
}

sub build_product {
    my ($product) = @_;

    say $product;

    # delete from hash
    delete $deps{$product};

    # delete from others who depend on it
    while ( my ($k, $v) = each %deps ) {
        $deps{$k} = [ grep { $_ ne $product } @$v ];
    }
}

open my $fh, '<', 'deps';

while (<$fh>) {
    chomp;
    insert_line_to_hash($_);
}

close $fh;

while ( my $next = get_next_product() ) {
    build_product( $next );
}

use Data::Dumper;
print Dumper( \%deps );

modules.pl

use strict;
use warnings;
use File::Find;
use Storable;
use v5.14;

my $counter = 0;
my $prev_counter = 0;

eval {
    my $info_ref = retrieve('counter.bin');
    $prev_counter = $info_ref->{counter};
};

sub count_txt {
    $counter++ if /txt$/;
}

find(\&count_txt, '.');

say "total: $counter";
say "diff: ", $counter - $prev_counter;
store ({counter => $counter}, 'counter.bin');