Adds partially implemented Action class.
More work on Action and implemented naive simulator.
Added test case replicating the 'abc.ka' model from the KaSim distribution. Needs review and testing.
Refactor State trait into Matchable trait, clean up equals implementation of {Pattern,Mixture}.Agent, replace Embedding argumant in Action.Atom classes by array, and general cleanup.
Adds missing changes from last commit: refactor State trait into Matchable trait, clean up equals implementation of {Pattern,Mixture}.Agent, replace Embedding argumant in Action.Atom classes by array, and general cleanup.
Work on positive updates. Compiles but not tested.
Rename PartialEmbedding class to ComponentEmbedding.
Adds 'join' and 'meet' operator to all Matchables.
Adds PartialEmbeddings class.
Adds positive update handling in Action. Needs testing and support in Model.run.
Adds remaining support for positive updates. Lazy negative updates do not seem to work, needs investigation.
Added classic negative update using lift sets in agents.
merged with master