Add a chapter on internal model structure and its configuration

[jrawbits]

Create a comprehensive reference to visioneval.cnf and how the VE environment, models and setups are organized. This chapter should also consider how to organize scenarios.

The things to consider:

1. visioneval.cnf in its various locations (runtime, model, model stage, scenarios)
2. detailed reference on all parameters possible for visioneval.cnf and where they can be applied
3. managing model organization with visioneval.cnf (folder names, results, model states, etc)

Some of that should be organized around user tasks, and some of it should be part of an encyclopedic reference of possibilities. User tasks:

1. basic model setup
2. organizing inputs and scripts
3. organizing stages and scenarios