Support incremental+inplace+transients case ('real' model reference during generation). Instead of in-place change of a model copy, and then propagating all the caches and updating 'internal' model references to 'visible',  we rather create and publish a snapshot of a model, and the model being changed goes through all the steps (with its model reference being updated as we move through steps).

Use common mechanism which decides whether to keep transient models with warnings
Complete deprecation of logger methods that take SNode. Update templates for generated generators to use new methods, regenerate uses.
Fix compilation issue with Java 6 on Windows (http://bugs.java.com/view_bug.do?bug_id=6302954)