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I have made an extension which, when installed, creates new tables and modify’s few existing tables of magento.
how to roll back these database changes in magento database when my magento extension is uninstalled from Magento Connect Manager?
I think you will have to do that manually. Normally you can see all the changes that have been made in your database in the SQL folder of your plugin:
app\code\local\Company\Module_name\sql\module_name_setup