Move the output code inside the @files loop

foreach my $file (@files) {
  my @output = ();
  print "\n Processing with file $file \n";
  open my $fh, '<', $file or die $!;
  my $count = 0;
  while (<$fh>){
    ++$count;
    # match any keyword
    if (/($re)/){
      my $kw = $1;
      push @output, [$kw,$file,$count,$_];
    }
  }
  close $fh;

  # sort by record timestamp
  @output = sort { $a->[3] cmp $b->[3]} @output;
  #pp \@output;

  # output
  my $outfile = 'output_'.$file;
  print "Check the output generated In file $outfile\n";
  open my $fh_out, '>', $outfile or die "$!";
  for (@output){
    my $kw = $_->[0];
    if ( defined $kwhashref->{$kw} ){
      print $fh_out "\n*******$kwhashref->{$kw}*******\n";
    }
    printf $fh_out '%s in file %s, line %d:%s'.$/, @$_;
  }
  close $fh_out;
}
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