Feature/issue 112

This pull request contains several fixes related to the generator.  

It fixes these two issues:

* fixes issue 112 by adding template parameter for whether to include Jacobian adjustment or not in log prob calculation

* fixes issue 151 by replacing size tests with dimensions tests

It also:

* refactored generated code so that there are no dependencies on agrad in the generated code, by
    * pulling the agrad-related functionality into static methods in model/util.hpp
    * refactoring assign() function to stan::math, simplify and roll in promotion
    * refactoring get_base1 and get_base1_lhs to stan::math
    * refactor fill() to stan::math
    * generalized is_uninitialized() to stan::math with specializations in agrad

* makes numerous little fixes in the generated code to simplify the model, including renaming some functions and removing others that weren't used

I've added a new wiki page on the generated model structure and utilities