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foreach my $entry (@file1) {
   $index{$entry} = 1
...
foreach my $entry (@file2) {
   $index{$entry} += 2;
}

foreach my $entry (@file1) {
   $index{$entry} = 1
...
   # '||0' is to still the warnings under 'use warnings'
   $index{$entry} += 2 if (($index{$entry}||0) < 2);
}