API development branch
Partial refactoring
Progress with the API
API update, run seems to work now
Examples 1 working
9 Example tests passing through API
Advance method extracted from run method
Added static methods to API to retrieve target and RunConfiguration.
ComponentTypes test still commented.
URLInclusionReader update
Merge remote-tracking branch 'origin/master' into api

Conflicts:
	src/main/java/org/lemsml/jlems/core/sim/Sim.java
Fix JarResourceInclusionReader
Java6
Merge branch 'master' into api

Conflicts:
	src/main/java/org/lemsml/jlems/io/reader/JarResourceInclusionReader.java
Merge branch 'master' into api

* master:
  Tidied up & formatted standard examples after testing on PyLEMS
  Readded option: -nogui, for running lems file (& saving results) without the graphics/plots
  Conditional example works in Pylems...
  Update README.md
  Adding warning in build.xml & info on where to generate docs
  added support for hyperbolic functions
  Improved handling of units with luminous intensity, j
  Adding constructors for Unit and Dimensions and some helper functions
  moved all visitors to org.neuroml.export. Needed ExpressionValued to implement IVisitable
  initial q and d implementation of ast visitors for C, python (supposed to be easily extensible). This will be used to preparse eqs exported by org.neuroml.export
  Added static strings for symbols in comparison nodes: public static final String SYMBOL = ".lt.", etc.
  Added method to set which class to use to lookup resources
Merge branch 'master' into api

* master:
  More verboste dumping of info from StateInstance on error
Updated to v0.9.6.0 after merging changes from master into api branch of @tarelli
Merge branch 'statedimensions' into api

* statedimensions:
  Ensuring all examples have attribute dimension in DerivedVariable
  Propagating dimensions into state types with a new method,
StateWrapper.getDimensionString() that returns the dimensionality as a
comma-separated string containing the dimension powers "m,l,t,i,k,n,j"
  spearating operator and function expressions.

Conflicts:
	src/main/java/org/lemsml/jlems/core/run/RuntimeRecorder.java
Minor changes to get api branch compiling
Removing any neuroml specific files & only testing on standard lems examples
Readding test CoreDependenciesTest; this will break the api branch!

This test on the "purity" of the org.lemsml.jlems.core was added by
@robertcannon to allow it to be used for GWT, so maybe move the api
classes to org.lemsml.jlems.api, @tarelli?