This fixes the following bugs:
- No longer overwrite the matlab-output files each step.
- Create output also for the initial state.
- Change filenames of matlab-output by one (initial state is 000.txt,
final state is NNN.txt and not (NNN-1).txt for total of NNN steps).
- Eclipse binary output matches eclipse output (includes the same
steps including initial state) for the same case.
Also added several comments outlining the parts of the run() function.