The short answer is that ~www/pdf/terraswarm/siteconfig.php defines:

// PDF file(s) used to augment prepublication uploads                                                                                
$siteConfig['prepublicationPdfAugment'] = array(
    "watermark" => "/home/www/terraswarmwww/resources/PrepubWatermark.pdf",
    "stamp"     => "/home/www/terraswarmwww/resources/PrepubStamp.pdf"
);

The solution is to edit those files, which are checked in to the main terraswarm website repo.

The longer answer is that /php/pubs/pubs.php contains:

// augment prepublication PDF file with additional info                                                                  
            if (isset($prepubFlag) && $prepubFlag && $mimeType == "application/pdf"
                    && isset($siteConfig['prepublicationPdfAugment'])) {
                $result = pub_pdf_augment($dbGroup, $table, $pubid, $upload_name,
                        $siteConfig['prepublicationPdfAugment']);
                if (!$result) {
                    $message .= "Error: failed to augment uploaded PDF file.
n";
                    $failed = 1;
                }
            }

pub_pdf_augment() is defined in php/include/pub.inc.php.

See also How does the prepublication facility work?".