The problem is this:
$diffTable->dropPrimaryKey();
> $diffTable->setPrimaryKey(array('foo'));
>
>
In MySqlPlatform->getPreAlterTableIndexForeignKeySQL the removedIndexes
are checked for auto columns. As the primary index is dropped only to be
added again, the auto column is not being identified and therefore not
adjusted.
I've filed a fix here: https://github.com/doctrine/dbal/pull/786
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