If you want temporary files to be moved to directory$_SERVER['DOCUMENT_ROOT']."/Uploads", you also need to modify cuteeditor_files\Dialogs\upload.php file.
Please open cuteeditor_files\Dialogs\upload.php and find the following code: $uploader->Name="UploadControl";
Add the following code so that you can specify a temp file location:
$uploader->TempDirectory="/mytempfolder";
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