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How to update Magento when the database structure changes between versions?

All the update methods that I saw (not sure about the magento connection method) do not apply to the database only with files and directories). I am in my first build of Magento, but I see that they changed the directory structure with past updates. So my question is: how do I upgrade Magento to ensure the database is updated?

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According to @Anton's answer, database updates are applied by PHP code in the Magento modules themselves.

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python, ruby ​​ - script, . , ( magento repos, dev, rsyncing , ) 5 1.3.2.4 1.5.0.1,

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