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

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

Now its consisten with python and C#

- Converted FileUtils zip methods to apache compress (or removed them)
- Git hash is now provided in run.cmake
Also a class name update (Proper casing)

# Conflicts:
#	src/java/pulse/cdm/system/equipment/mechanical_ventilator/SEMechanicalVentilator.java
#	src/java/pulse/utilities/csv/plots/ActionEventPlotter.java
#	src/java/pulse/utilities/csv/plots/ConvexHullPlotter.java
#	src/java/pulse/utilities/csv/plots/MultiPlotter.java
#	src/java/pulse/utilities/csv/plots/RespiratoryPFTPlotter.java

Rebase from substance initialization in mech. vent., airway name change, and shorten hemorrhage groups

Pulse will now derive the format based on filename extension

Doesn't fix a default warning, but it's canonical after 1.7, at least until Java 11. It generally makes the code easier to read.

While this doesn't fix a default warning, it's canonical and people expect it. It also makes the code easier to understand.

Note that I did this using Eclipse's automatic import cleanup, which also made lots of changes that do not fix warnings (e.g., expanding wildcards, etc.).