A Lucky Find!

This splendid (but typical) example has several new red flags:

        Subject: Re: Use of uninitialized value at ...... warning with hash of hash
        Message-Id: <37A17F79.36E82AF5@ebi.ac.uk>;

          my($each_sub, %out_subs, %left_out, $ver, $real_sub_entry_found,
             %final_out_subs, %out_subs, $separate_hash_entry_opt, $long_subname,
             @final_separate_entry_out);

          #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          # Parsing input files of perl programs
          #_____________________________________________

          my @lib = @$lines;

          #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~``
          #  This for loop does not allow return until each sub is finished
          #_____________________________________________________________________
          for ($j=0; $j < @lib; $j++) {

            #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~`
            # Reading the first delimiter line and 'Title' line altogether
            #_______________________________________________________________
            if ($lib[$j]=~/^\#[\-_]{50,}/ ) { 
              next;
            } elsif ( $lib[$j]=~/^(\#+ *title *: *([\w\-\.]+))/i ) {
              $long_subname=$1;  $sub_name=$2; $title_found=1;
              if ($sub_name=~/\.pl$/) {
                next;
              }                         ## to avoid the very first headbox
              $out_subs{"$sub_name"}{'title'}="$sub_name";
              ...
            }
            ...
          }