Cleanup WHAT?

I do presently have my blog upgraded to 2.6.3 but I still get the message that “Cleanup is not complete”. When I follow up on that I am directed to wpau-upgrade.class.php line 440

Now elsewhere here I have seen reference to the ‘Cleanup’ being simply to remove backed-up files from Wau-backup folder, which were created during the Auto Upgrade process. But all I have in my Wau-Backup folder is an Index file containing the text ‘silence os golden’. Excuse lack of exact syntax here – but you get the thrust of what I am saying.

Investigation of wpau-upgrade.class.php line 440 reveales:
function cleanUpProcess() {
if(file_exists(trailingslashit(ABSPATH) . WPAU_LOG_FILE)) {
410 unlink(trailingslashit(ABSPATH) . WPAU_LOG_FILE);
}
if($dir = @dir($this->theDirToDoThings)) {
@chmod ($this->theDirToDoThings, 0757);
$this->recursive_remove_directory($this->theDirToDoThings);
return true;
}
else {
return false;
}
420 return false;
}

function recursive_remove_directory($directory, $empty=FALSE) {
if(substr($directory,-1) == ‘/’) {
$directory = substr($directory,0,-1);
}
if(!file_exists($directory) || !is_dir($directory)) {
return FALSE;
430 }
elseif(is_readable($directory)) {
$handle = opendir($directory);
while (FALSE !== ($item = readdir($handle))) {
if($item != ‘.’ && $item != ‘..’) {
$path = $directory.’/’.$item;
if(is_dir($path)) {
$this->recursive_remove_directory($path);
}
else{
440 unlink($path);

So WHAT do I need to manually “Clean Up” in order to be able to use the Automatic Upgrade at a future date when for instance, 2.7.- is automated???