Web updater is broken in extension registration.
steps to reproduce this step is the normail way using require
require_once ( "$IP/extensions/CheckUser/CheckUser.php" );
then go to mw-config on your website then go through step and click next on upgrade look through the log when the updater is finished there should be cu_ prefix meaning that the sql for checkuser was done.
This step is for extension.json to show difference.
wfLoadExtension( 'CheckUser' );
then go to mw-config and go through steps then you should get to the upgrade page.
Then click next and look through log once finished it should show cu_ prefix but there isent any because it didn't work with extension registration. I am also having this problem with math at https://gerrit.wikimedia.org/r/#/c/187654/ please fix problem.