By using a hash as per the FAQ, the intersection/difference calculation will be order-independent. You will have to compare the resulting hash (called %count in the FAQ) against a given file's content to determine which file lacked the line in question. Note that the FAQ's code fails if either array has repeat entries.

Alternatively, you can use bit operations rather than simple incrementation to encode a little extra info. The FAQ code structure is more immediately obvious, but this may do more of what you want:

#!/usr/bin/perl
use strict;
use warnings;

my $master = shift;
my $completed = shift;

open my $mh, '<', $master or die "Open fail on $master: $!";
my @master_lines = <$mh>;
chomp @master_lines;

open my $ch, '<', $completed or die "Open fail on $completed: $!";
my @completed_lines = <$ch>;
chomp @completed_lines;

my %count;

for my $element (@master_lines) {
    $count{$element}|=1;
}
for my $element (@completed_lines) {
    $count{$element}|=2;
}

print "$master only:\n";
for my $element (@master_lines) {
    next if $count{$element} & 2;
    print "$element\n";
}

print "$completed only:\n";
for my $element (@completed_lines) {
    next if $count{$element} & 1;
    print "$element\n";
}
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