my @line;
my %third_col;

while( <> ) {
    chomp;
    my @col = split /\|/, $_, -1;
    my $key = join '|', @col[ 0, 1 ];

    push @line, $key if not exists %third_col{ $key };

    push @{ $third_col{ $key } }, $col[ 2 ];
}

for ( @line ) {
    print $_ . '|' . join ',', @{ $third_col{ $_ } };
}
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Makeshifts last the longest.