MPG vignette improvements

[achubaty]

Improve documentation of Engine class and methods to make it easier to come back later to diagnose C++ problems.

• add call graphs generated from code for easier updating (7aee2b9);
• add class diagrams generated from code for easier updating;
• add flow diagram generated from code for easier updating;

how to automatically produce call graphs and class diagrams? would be great to generate these from the C++ directly rather than having to manually update the vignette.

• add section on debugging C++ in R package;