Tidying classes in src/idyno
Tidying classes in src/povray
Tidying classes in src/agent
Tidying classes in src/agent/zoo
Tidying classes in src/simulator
Tidying classes in src/simulator/detachment and src/simulator/diffusionSolver/*
Tidying classes in src/simulator/geometry/*
Tidying classes in src/simulator/reaction/*
Tidying classes in src/utils
Tidying example protocol files
Merge pull request #56 from roughhawkbit/master

Tidying up