I was going to look into this, but i absolutely hate, hate implicit the use of $_. It makes the code so much harder to read and so much harder to understand and so much harder to follow. I prefer it more like this:

#!usr/bin/perl

use strict;
use warnings;

open my $wave,    '>', 'Wave' or die "Can't open $wave: $!";
open my $keywords,    '<', 'Agents' or die "Can't open keywords: $!";
open my $search_file, '<', 'Definitions'   or die "Can't open search f
+ile: $!";

# Urgh, that following line needs serious reformatting,
# It's still an ugly mess that is very hard to understand at a glance
my $keyword_or = join '|', map {chomp;qr/\Q$_\E/} <$keywords>;

my $regex = qr|\b($keyword_or)\b|;

while((my $line = <$search_file>)) {
    if($line =~ /$regex/g) {
        if ( $line =~ /(SCRIPTNAME|DESCRIPTION)/ ) {
            next;
        }
        print $wave $line;
        
    }
}   
close $wave;
close $keywords;
close $search_file;
[download]

Still less the ideal, but at least i could start to follow the data around.