Fix output statements in SimulatorFullyImplicitBlackoil::run().

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.

NOTE: after merging this, output files used for regression tests should be regenerated, since their names have been changed (increase number by one) relative to before.