Migration command depends on extension manager which makes updating from 3.0 impossible

PHP Fatal error: SQL ERROR [ sqlite ]<br /><br />SQL logic error or missing database [1]<br /><br />SQL<br /><br />SELECT *
FROM phpbb_ext in /var/www/try-phpbb.com/31x/phpbb/db/driver/driver.php on line 844

When trying to update from 3.0 with CLI.