jdbc/Main tables are created by default on startup. To disable this behavior, you should add the deployment parameter init_db and set it to false in the application context file.
This feature is not available for other data sources, which are always assummed to be managed outside the scope of the application.
If the above differs from you experience, please provide additional info, such as the application context file, and details of the specific schema changes which do not comply with the above description.
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