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  ( $dir, $file ) = m/(.*)[\\\/](.+)/ ? ( $1, $2 ) : ( undef, $_ );
#  print "$file is in the directory $dir\n";
  $fileinfo[$i] = [$file, $dir];

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    $refarray1 = $fileinfo[$c];
    if (${$refarray1}[0] eq $intersect) {
      print "File: ${$refarray1}[0] in directory ${$refarray1}[1]\n";
      $matchedfiles[$i] = [${$refarray1}[0], ${$refarray1}[1]];
    }

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      $matchedfiles[$i++] = [${$refarray1}[0], ${$refarray1}[1]];

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my %md5_of_known_bad;
foreach $md5data (@knownbad) {
  ...
  $md5_known_bad{$filename} = $md5hash;
}

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  if (exists $md5_of_known_bad{$filename}) {
     # $filename is a known bad
  }

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my @uniq;
@uniq = grep { exists $md5_of_known_bad{$_} } @sysfiles;