MDEV-32462: mysql_upgrade -s still checks for non system tables

- Rename files as requested by Vicentiu:
```
 mysql_json_mysql_upgrade.test                    -> mysql_upgrade_mysql_json.test
 mysql_json_mysql_upgrade_with_plugin_loaded.test -> mysql_upgrade_mysql_json_with_plugin_loaded.test
 mysql_json_mysql_upgrade_system_tables.test      -> mysql_upgrade_mysql_json_system_tables.test
```
- Related to PR #2790
- Reviewer: <daniel@mariadb.org>, <vicentiu@mariadb.org>