Initial commit
Added user guide
Modified grammar to be compatible with a subset of KaSim grammar.
Work in progress - still %mod (and other) to do.
Converted to work with KaSim Kappa grammar - work in progress.
<-> transform rules no longer allowed
SpatialTranslator now outputs %agent rules & correct location indices.
Modifications to grammar to be more compatible with KaSim
Addition of mean and standard deviation chart for compartments
Updated record and replay file formats to match plot data format of
KaSim
Some refactoring
Started updating documentation.
Updated version number
Fixed minor command line bug in SpatialTranslator.
Created PlotViewer to quickly view Kappa plot output files.
Fixed replay handling of INF and NAN in plot data files
Handle output of -NAN and -INF in plot output files.
Updated spatial description syntax for PSD stage 1.

- Compartments are now ids instead of labels.
- Location can be specified at either rule or agent level - agent
  location taking precedence.
- PSD stage 1 acceptance tests - work in progress.
Added more PSD stage 1 acceptance tests.
Input Spatial Kappa now uses (and requires) %agent: declarations

Bug fix - SpatialTranslator correctly outputs ? link types
Bug fix - SpatialTranslator correctly outputs variable declarations in
original order
Bug fix - Spatial Kappa parser can handle end of line comments
Bug fix - Spatial Kappa parser can handle empty input files
Added PSD stage 1 acceptance tests
Substantial modifications to Spatial Kappa syntax, and translation
application.

Changes were made to produce the PSD 2.0 Stage 1 deliverable and
included:
- changed Spatial Kappa grammar to allow located agents and named
channel agent links
- acceptance tests for stage 1
- code modifications to the translation application to make use of new
Spatial Kappa syntax
Added release notes and user manual for the translator.
%channel: declarations are now more consistent and logical.

%channel: declarations now composed of multiple forward only links.
User manual updated to reflect changes in syntax.
Cleaned up use of %channel: in translator.
Relocated some methods from SpatialTranslator to KappaModel.