2 Joomla, :
1) Just put your SQL changes (e.g. ceate table or alter or any thing) /administrator/components/com_admin/SQL/updates/YOU_DB_ENGINE/anyfilename.sql go to the web interface, then / administrator => extension => manage => database and simple fix.
2) you can take a look at / administrator / components / com _installer / models / database.php and implement the custom migration process on it so that you can use the custom folder
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