Created a mess with getVolumeCounts.m, about to simplify a bit
Near finished version of getVolumeCounts.m, going to test fancy version one last time ...
Removed NEURON class, hopefully simulations will no longer launch when doing tab complete.
This issue might be fixed when moving simulations to being just below NEURON package
Added try catch on delete for handle_light to try and debug warning message that occasionally pops up for handle class
available_options.m - added a note to fix this ...
general_sim_definitions.hoc - Added binary data transfer path for writing to scratch path instead of writing to git directories ...
Cleaned up Java Comm Object to not require hiding a window in Windows
Major change to simulation structure. This is the first functional commit (I think) of the code which moves the old NEURON class to the simulation class. NEURON static methods are now in their own package.
Added temporary function init_system for redirecting initialization and warning of change ...
windows_comm_obj.m - changed initialization procedure given changes to java comm object
Removed references to windows specific installation scheme
Updated user_options to use pointer to NEURON executable
Updated documentation for extracellular_stim_capable.m
Nearly finished with Stimulus Interaction paper
mass commit of simulation code ...
final commit of updates ...
Some additional tests for the stimulus interaction paper and better printing of the status for getThresholds
Merge branch 'master' of https://github.com/JimHokanson/matlab_NEURON

Conflicts:
	matlab_code/+NEURON/@paths/paths.m