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.).

Switched from using clone to just directly constructing the desired type, which fixes a cast warning

Note that clone() is not something that gets used often -- probably best to avoid it.

The way it was before, if an exception was thrown, the resources would not have been closed. When using this method, there is no need for an explicit close.

They are deprecated starting in Java 9, which probably won't be updated to any time soon, but it's nice to fix these as they are seen.

Replaced OrderedProperties implementation with an existing open source one. Eliminates a lot of warnings.

The author claimed it fully implemented the methods in Properties, but it did not fully implement the methods of the HashTable base class. So I had to tweak a couple of lines elsewhere to work with the new implementation.

A  few other implementers needed to implement some now-abstract methods, or switch to use the public methods.

As it was before, throwable messages would just get printed. Slf4j has its own built-in throwable handling; notably, the stacktraces are captured.

I included the logback jars so something actually shows up in the console. Those, and the slf4j jar, are only needed for the HowTo.
Note that the log levels don't quite line up, so nothing is logged to trace, and the fatal messages are logged to error with a "FATAL: " prefix.

By default, have an engine log to the console
(Loggers, by default, do not)

Also added const protection to substanes retrieved by users from the engine

Updated system fidelity figure.