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Remove the schema shell. I don't think we are going to have time to build a proper replacement for 3.0.0. I also think that migrations are something that would be better handled in a plugin where ideas can be iterated more quickly and compatibility constraints are less strict.
Once the main development push for 3.0 settles down I'd like to properly revisit migrations and possibly extend/enhance existing solutions like cakedc/migrations instead of building yet another migrations tool.