Initial version of functions to allow integration with NEURON
Fixes to get compilation working
Improved documentation
Added overrideInitialValue()
First attempt at runByTime2()
Allow initial value to be zero
Debugging output to find out about crash with large numbers
TransitionInstance.activity as long rather than int
Fix compilation
Turned off verbosity
Fix for ConcurrentModificationException

This arose due to iterating over a list that might be modifiable. The
fix is to define an iterator over the list and use Iterator.remove()
rather than List.remove().
Converted to Makefile format
Renamed to Makefile
Merge branch 'neuron' into python