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use File::Slurp;
my @file1 = read_file('file1');
my @file2 = read_file('file2');

my $lines = merge_lines(\@file1, \@file2);
write_file('file3', @$lines);

sub merge_lines {
    my ($lines1, $lines2) = @_;
...
    ....
    return \@lines;
}