Small tweek to glucose generation in tissue
Update namespaces in validation tool
Fix bug in Convex Hull plotter
Fix bug in Multisource plotter
Remove the old 12hr baseline

- Found by running a condition with 0 severity (should be the same as BasicStandard)
- Added a scenario for each patient condition with 0 seveirty to make sure that does not happen again
Fixed an issue with Java Logging to where it does not report errors
Removed a few hemorrhage scenario's that are now redundant

Merge branch 'feature/documentation' of https://gitlab.kitware.com/physiology/engine into feature/documentation

Merge branch 'feature/documentation' of https://gitlab.kitware.com/physiology/engine into feature/documentation

Updates to cardiovascular and endocrine matrices. Updates to cardiovascular and endocrine methodology reports.

- Update Python/C#
- Finish serialization

Merge branch 'feature/documentation' of https://gitlab.kitware.com/physiology/engine into feature/documentation

Refactor Action/Condition managers and collections, and PulseConfiguration AND Patient Configuration ctors not accept a Substance Manager
- Pushed that requirement to methods that need it and to be provided by the caller
Should simplify construction and usability of these various classes (especially conditions)
Also changed Data request creation to take substance names, and not substances (no need to load things off disk to fill out a name)

Update Hydrocephalus study outputs and added in all overrides
Simplified our full preliminary data combination set
Added in a python analysis file to be filled out

#Additionts
#            Refactor PulseConfiguration to move SubMgr from ctor to Serialize methods

# Conflicts:
#	.gitignore

Update Extended Language API's

See merge request !46

Ensure all actions/conditions are supported througout processing

Add more comments in using it into our HowTo

Clean up Java
 -- No more deinitialize
 -- No native initialize
 -- pullData returns a List<Doulble> now

CDM2MD uses reflections which uses the javassist jar