Update.  As it seems that my wordpress instance does not have the 'wp_'
prefix on most of the database tables, it was 3 new lines in the updated
/etc/wordpress/wp-config.php that caused the problem:

if (!isset($table_prefix)) {
    $table_prefix = 'wp_';
}

The fix was to restore the wordpress database from backup and then add
one line, setting $table_prefix to '' in my site's /etc/wordpress
/config-default.php where the database passwords are.

$table_prefix = '';

And then run the Automatic Updater normally:
http://localhost/wordpress/wp-admin/update-core.php

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https://bugs.launchpad.net/bugs/990615

Title:
  wordpress upgrade failed. drops to install screen. database schema not
  upgraded

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