Add stack for operations

Up and down operations should only put commands on a stack that is then executed after up() or down() have been processed.

Currently there are two implicit stacks:

1. addSql()
2. The changes done to the $schema instance.

With DMIG-26 $schema is an explicit change that adds to a stack.

This should be unified to be one single stack called "operations" and they should be linearly processed.