* removed model_list getters from context class. model list is now entirely
  context-private

* removed GetModelByName from context class. Changed it's only usage in
  region_model to use CreateModel instead and had xml_file_loader AddPrototype
  for all models to make this possible.

* Created context::KillModel method that should be used for all model
  deallocation/termination.

* Moved global model teardown/deallocation out of the timer::RunSim and into the
  context destructor.  This removed necessity for manual deletion of model
  pointers in all tests.

* Removed manual context::AddModel method.  Now all calls to
  context::CreateModel and context::AddPrototype automatically add a model to
  the model_list_.  Fixes #642.
fixed dealloc delete sequence issues. Added IOError exception throw on hdf5 error. minor tweaks.
made context model management more universal. Made model_list_ a std::set. added doc comment about context model management. minor tweaks
fixed all tests. still need to check running full sims
fixed deploy self as parent bug in xmlfileloader. Model class removes 'this' from context model_list_ in destructor to prevent some segfaults when models are allocated on the stack causing a double delete (one by runtime and one by context). Put guard on context::DelModel to only delete if the model is in the model_list_
renamed InitCoreMembers to InitFrom
changed xml Init[Core/Module]Member fan methods to be InitFrom chain. Gave model class a default val for model_impl_ to facilitate testing of xml init methods.
changed clone methods to use context-arg constructor
removed some unneeded methods and changed some doc comment style in model.h
finished changing comment style in model class. Removed SetModelType method. Renamed ModelType to model_type
added note about subclass model_type_ var setting
added more detail about context model ownership and stack models are bad.
Merge pull request #691 from rwcarlsen/api-cleanup

tightening up context api