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open (my $in, "<", $ARGV[0]) 
    or die "in: $@";
...

close $in;
close $out;

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open (my $in, "<", $ARGV[0]) 
    or die "in: $@";

my @lines = grep { not /^#/ } <$in>; #<> here in list context, therefo
+re no explicit loop