empty lines added in patches are lost

...which throws off the line numbers.

looks like this is to blame:

      else if (preg_match("/^\+[^\+]+/", $line)) {
        $patch .= ltrim($line, '+') ."\n";
        $in_patch = 1;
      }

the regex looks like it wants to skip the lines beginning with +++ but it also skips a single + on its own