As an alternative, read line by line and decide for each type what to do:

use strict;
use warnings;

while(<>){
    print and next if /^\d+\s/;
    chomp;
    print          if /^([A-Z]+|[.]+)$/;
    print "\n$_"   if /^S+[.]*$/;
    print "\n"     if m|^//$|;
}
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