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my @file1 = <FILE1>;
my @file2 = <FILE2>;
...
        print FILE3 "$value\n";
    }
}

# Using the same data structures as above ...
foreach my $value (sort keys %file2) {
...
        print FILE3 "$value\n";
    }
}

my (%file1, %file2);
$file1{$_}++ foreach @file1;
$file2{$_}++ foreach @file2;