Modified path upgrade script for contao. No config editing necessary. Copy in your Contao root and run.

contao-db-update.php

<?php

/*
	When updating from Contao 2 to Contao 3, you must not rename the tl_files folder to files! 
	If you want to re­name the folder, you have to take the following steps:

	· Complete the version 3 update in the install tool
    	· Then rename the upload folder in the back end settings to files
    	· Last run the modified version of Tristan's script

	If you do not want to rename the directory, the name of the upload folder remains tl_files, 
	also in Contao 3. This does not apply to fresh installations of course.
*/

define('TL_ROOT', '/');
require 'system/config/localconfig.php';

// Database credentials
$strHost 	= $GLOBALS['TL_CONFIG']['dbHost'];
$strUser 	= $GLOBALS['TL_CONFIG']['dbUser'];
$strPassword 	= $GLOBALS['TL_CONFIG']['dbPass'];
$strDatabase 	= $GLOBALS['TL_CONFIG']['dbDatabase'];

// From and to path
$strFrom = 'tl_files/';
$strTo = 'files/';

// DO NOT EDIT ANYTHING BELOW THIS LINE UNLESS YOU KNOW WHAT YOU ARE DOING!

error_reporting(E_ALL ^ E_NOTICE);

function array_strpos($arrHaystack, $strNeedle)
{
	foreach ($arrHaystack as $v)
	{
		if (is_object($v))
		{
			$v = get_object_vars($v);
		}

		if (is_array($v) && array_strpos($v, $strNeedle) || !is_array($v) && strpos($v, $strNeedle) !== false)
		{
			return true;
		}
	}

	return false;
}

function array_str_replace($strSearch, $strReplace, $arrData)
{
	foreach ($arrData as $k=>$v)
	{
		if (is_array($v))
		{
			$arrData[$k] = array_str_replace($strSearch, $strReplace, $v);
		}
		elseif (is_string($v))
		{
			$arrData[$k] = str_replace($strSearch, $strReplace, $v);
		}
	}

	return $arrData;
}

try
{
	$db = new PDO
	(
		'mysql:dbname=' . $strDatabase . ';host=' . $strHost,
		$strUser,
		$strPassword,
		array(PDO::MYSQL_ATTR_INIT_COMMAND => "SET NAMES 'UTF8'")
	);

	$stmt = $db->query('SHOW TABLES');
	$stmt->setFetchMode(PDO::FETCH_COLUMN, 0);

	foreach ($stmt as $strName)
	{
		$arrTables[] = $strName;
	}

	$intUpdates = 0;

	if (substr($strFrom, -1) == '/' && substr($strTo, -1) != '/')
	{
		$strTo .= '/';
	}
	else if (substr($strFrom, -1) != '/' && substr($strTo, -1) == '/')
	{
		$strFrom .= '/';
	}

	echo 'Searching tables' . "\n";

	foreach ($arrTables as $strTable)
	{
		echo 'Processing ' . $strTable . "\n";

		$stmt = $db->query(sprintf('SELECT * FROM `%s`', $strTable));
		$stmt->setFetchMode(PDO::FETCH_ASSOC);

		foreach ($stmt as $row)
		{
			foreach ($row as $k=>$v)
			{
				$blnSerialized = false;
				$tmp = unserialize($v);

				if ($tmp !== false)
				{
					$blnSerialized = true;
					$v = $tmp;
				}

				if ($k != 'id')
				{
					$w = false;

					if (is_object($v))
					{
						$v = get_object_vars($v);
					}
					if (is_array($v) && array_strpos($v, $strFrom) !== false)
					{
						$w = array_str_replace($strFrom, $strTo, $v);
					}
					if (!is_array($v) && strpos($v, $strFrom) !== false)
					{
						$w = str_replace($strFrom, $strTo, $v);
					}

					if ($w)
					{
						if ($blnSerialized)
						{
							$v = $row[$k];
							$w = serialize($w);
						}

						$stmt = $db->prepare(sprintf('UPDATE `%s` SET `%s`=:value WHERE `id`=:id', $strTable, $k));
						$stmt->bindValue('value', $w);
						$stmt->bindValue('id', $row['id']);
						$stmt->execute();

						++$intUpdates;
					}
				}
			}
		}
	}

	echo 'Update finished: ' . sprintf('%d rows updated', $intUpdates) . "\n";
}
catch(PDOException $e)
{
	var_dump($e->getMessage());
}