Refactored Transformer and TransformCommand

The goal of this refactoring was:

1. To move all output logic (logging) from the Transformer back to
   the TransformCommand using events.
2. To allow writers to initialize themselves or the ProjectDescriptor
   before all transformations are executed. This allows writers to set
   up globals and other state using the ProjectDescriptor that other
   writers could use. An example is the upcoming Search writer that can
   inject a partial to show a search box tailored to a specific search
   type.
3. To move behaviours out of the Transformer as to make it more lean
   and loosen dependencies.
4. To clean up the code of the Transformer
Yes, the PRE_TRANSFORM is called before _all_ transformations are executed; and the PRE_TRANSFORMATION event is called before each individual transformation