Started to addfraeork to have CPPNodes with a Function rather than a parameter like the current NeatNodes
Started framework for CPPNNodes which works in a similar manner to NeatNode
Framework for CPPNFunction with Parabola function
Sine, Parabola, and gaussian distribution graphs can all be modeled with just 3 variables in the CPPNFunction class
Added sigmoid function and some clearing up
More stuff
Real update
Added CPPN skeleton files.

CPPN function node classes are not currently fully implemented, nor is
the CPPN class that calculates a network output given a tuple of inputs.
Removed hidden files.
More HyperNeat implementation.

Each CPPN node now encapsulates a CPPNFunction object; this is for
future consideration of calculating total network output (accumulating
each node's function instance for example).
Started process of creating agents with a basic set of genomes, which will create a set of CPPNs to generate a brain
More stuff
More skeleton stuff, starting to flesh parts out. Agents now have a lot of the set up code put in
I think all the framework is there, it just needs the actual code to be implemented now... I think
More fleshing stuff out in CPPNFactory
NeatNodes now encapsulate CPPNFunctions.

Each NeatNode in Ruth's genetic package now encapsulates a CPPNFunction.
The CPPNFunction parameters are also mutated by the GA, and `add-node'
mutations create new NeatNodes that encapsulte a random CPPNFunction
with random parameters.

This does need testing though as other tasks need doing before we can
compile.
Lots of changes. Removed CPPN Edges, because with the parameter A they were unnecessary, this simplifies the genomes as well, which is good. CPPNSimulation and factory should be working, cant test until the genetics stuff has been finished though.
Added comments to explain what parts need to be done and roughly how they should be done
Added more comments
put ArrayList<Genome> inside Chromosome class so species id and parents can be held once for each agent