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while (<>) {
    chomp;
    $no_dupes{$_} = $. if (! exists $no_dupes{$_});
}

use strict;
use warnings;
...
            keys %folded_lines;

print RESULT_FILE $_, ': ', join( ', ', @$folded_lines{$_} ), "\n" for
+ @dupes;

foreach ( @dupes ) {
    print RESULT_FILE
...
        join( ', ', @{$folded_lines{$_}}[ 1 .. $#{$folded_lines{$_}} ]
+ ),
        "\n";
}

don't panic: 34, 55, 89, 144