Checking in CellML models

Thanks for extracting the CellML models from the site Graham. Checking
them in so we can all easily access them.
Updating cfg text files

The format of these files kept changing every time I synced, so checking
them in with the updated format. If this throws anyone else off we can
come up with a different solution. This is the quickest fix, I think.
Unit tests

This check in adds the JUnit unit test framework to SemGen. We can now
add unit tests. I've created a unit test class for CellMLReader that
contains a default unit test that always passed. Next I plan on writing
a simple unit test to verify reading cell my files works properly
CellML Reader Unit tests

Adding a couple unit tests for the CellML reader. Here's what they do:

1) Verifies the reader can read a file successfully
2) Verifies the pubmed annotation is read properly

There are many many more tests that should be added. This should get us
started.
Fixed crlf issue
Get stats for cellml files

script to build a csv file containing data about variables in cellml
files
Remove guyton models

Remove guyton models from examples dir
Update data script

Issues:
1) Script wasn't getting enough useful information
2) Script was taking too long to run

Improvements:
1) Get one row per variable per file
2) Categorize variables by model and model category
3) Parallel process files to make things a little faster

Things that would be nice to have:
1) Move the job script to a different ps1 file
2) Improve code that manages jobs
Lower sleep time

Decrease the sleep time so we generate more jobs in parallel
The line for retrieving the bioportalid in ReferenceClassFinderPanel had
been accidentally erased, making it impossible to search for terms on
BioPortal.
Fixed bug that was preventing the Composite Annotation Component Search
Dialog from opening.
D3 graphs

With these changes SemGen can now support loading variable dependency
relationships in d3 graphs. The directed graph is currently the only
graph that works. However, other graphs are coming soon.
Merge branch 'master' of https://github.com/thompsct/SemGen

Resolved classpath conflicts
Merge branch 'Refactoring'

Conflicts:
	cfg/ontologyTermsAndNamesCache.txt
	cfg/startSettings.txt
	src/semgen/SemGenGUI.java
	src/semgen/annotation/Annotator.java
	src/semgen/annotation/CodewordButton.java
	src/semgen/annotation/ReferenceClassFinderPanel.java
	src/semgen/annotation/composites/CompositeAnnotationComponentSearchDialog.java
	src/semgen/extraction/ExtractorTab.java
	src/semgen/visualizations/D3.java
	unitTests/semsim/reading/CellMLReaderUnitTests.java
Fixed an oversight which was allowing a file to be annotated when it was
already open in another annotator tab.
Added comments to quite a few classes.