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ALTER TABLE in Magento setup script without using SQL

Jonathon Day says

“updates SHOULD NOT be in the form of
SQL commands”. I haven’t come across
any DDL or DML statments that cannot
be executed via Magento’s config
structures.

(In the question How can I migrate configuration changes from development to production environment?)

I would like to know how best to add/modify/remove a column or index to/from a table in this manner, but without relying on SQL? Is it even possible?

Furthermore, what other actions can only be done in SQL?

ALTER TABLE in Magento setup script without using SQL

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