By the way,

my %seen;
my @uniq;
foreach my $item (@lines) {
        unless ($seen{$item}) {
                #if we get here, we have not seen it before
                $seen{$item} = 1;
                push(@uniq, $item);
        }
}
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can be written as

my %seen;
my @uniq = grep !$seen{$_}++, @lines;
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