fixes #617
fixes #681
* 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.
removed extra line
Merge pull request #690 from scopatz/no-cmake

fixes #617
add better doc comment details to Material::ExtractComp. Fixes #664
fixed dealloc delete sequence issues. Added IOError exception throw on hdf5 error. minor tweaks.
Merge pull request #692 from rwcarlsen/664

add better doc comment details to Material::ExtractComp. Fixes #664
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
fixes #639
Merge pull request #693 from scopatz/headgaurd

fixes #639
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.