Format cleanup

# Conflicts:
#	src/cpp/impl/multiplex_ventilation/main.cpp
#	src/python/pulse/cdm/utils/plotter.py

Updated Python plotting

Modified manual running of multiplex ventilation analysis to easily allow for any number of patients.

Change from using the plt object directly to using a subplot which will
be able to be put into a list for later usage.

The list should be a dictionary of column name to plot for column.

Update the "__main__" usage to properly take the list and pass it to
save images.

Add in the tick formatting which will use scientific notation for the Y
axis.

Add a start of a new plotting utility.

On "to do" list:
 Find the right way to save a list of plots
 Be able to toggle between showing plots and saving plots
 Set Y-axis in scientific notation
 Put legend to reside under title

Add the capability to add a "Pulmonary Shunt" condition and and
exacerbation of that condition as a patient action

Add the pulmonary shunt condition and the exacerbation of that condition
as a patient action.

Include a HowTo file for both new classes.

Add the systems and properties necessary to support Scalar Overrides
from the Python interface.

There should be an override property for both Patient Configuration and
for patient actions.

Cleaned up where things output

PIP is now directly solved.
O2 stabilization is a little different.

 - Moved Clears to the Load, and Setups as well, both to be called BEFORE the serialize method, so things are clear, and internal (non serialized) variables are setup before we serialize and lastly, state change
 - Airway mode was not correct in the engine as anesthesia machine was not coded to play well with others wanting to modify airway mode (ventilator) so now both of those two are getting along better
 - Clear out ventilator substance fractions when meging (comment in code as to why)
 - Added serialization of respiratory overrides
 - Exposed another model parameter from respiratory

- Need to fix discovered serializtion bugs!

# Conflicts:
#	src/python/pulse/cdm/io/patient_actions.py
#	src/python/pulse/cdm/patient_actions.py

# Conflicts:
#	src/cpp/impl/multiplex_ventilation/MVGenData.cpp

Add the classes necessary to utilize the ConsciousRespiration patient
action.

Add a howTo which sets an example usage of the Respiration action.

Added some helpful comments.

Allow adding nodes/paths/cmpts/links with the same names
Refactor multiplex engine to use the proto structures

There are still a couple of to-dos and it needs to be tested.

Fixed enum change in python files.