reverting the reorganization done in 3455-3456 in order to make merging my experimental branch to trunk easier.

Preparation for new organization of code in to sub packages. Changed autoload() to work with new structure.

some small refactorings. adding docblocks. creating guard clauses. refactor our some code into methods. no aditional test failures so it looks ok. also added some @todo comments

Fleshing out functionality of CLI system and changed syntax of migration classes to only required a to parameter since we already know where we are coming from.

small migration fix (notice+warning when the migration folder is empty because of uninitialized variable)

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