Configure transactions manually on <3.12

[adamnovak]

The "DEFERRED" isolation_level we use on Python 3.12 doesn't actually seem to put table schema changes from the migrations into a transaction we can roll back.

This adds an explicit "BEGIN DEFERRED" which makes the schema changes go away when we rollback(). This very much does not "start a transaction" (see https://sqlite.org/forum/forumpost/98f04f5585b83eb1), so I'm not sure why it works if the database is really in the "DEFERRED" isolation_level which is supposed to be basically the same thing.

Changelog Entry

To be copied to the draft changelog by merger:

• Toil history database now uses transactions properly for schema changes on Python <3.12.

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