upload.php

<?php
$output_dir = "uploads/";
if(isset($_FILES["myfile"])) {
	$ret = array();
	
	//	This is for custom errors;	
	/*	$custom_error= array();
		$custom_error['jquery-upload-file-error']="File already exists";
		echo json_encode($custom_error);
		die();
	*/
	$error =$_FILES["myfile"]["error"];
	$thisTS = time();
	//You need to handle  both cases
	//If Any browser does not support serializing of multiple files using FormData() 
	if(!is_array($_FILES["myfile"]["name"])) { //single file
 	 	$fileName = $_FILES["myfile"]["name"];
 		#move_uploaded_file($_FILES["myfile"]["tmp_name"],$output_dir.$fileName);
 		move_uploaded_file($_FILES["myfile"]["tmp_name"],$output_dir.$thisTS.".pdf");
    	#$ret[]= $fileName;
    	$ret[]= $thisTS.".pdf";
	} else {  //Multiple files, file[]
	  $fileCount = count($_FILES["myfile"]["name"]);
	  for($i=0; $i < $fileCount; $i++) {
	  		$fileName = $_FILES["myfile"]["name"][$i];
	   	move_uploaded_file($_FILES["myfile"]["tmp_name"][$i],$output_dir.$fileName);
			$ret[]= $fileName;
		}
	}
   echo json_encode($ret);
}
?>