Fix output statements in 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.
Merge pull request #183 from atgeirr/fix-output

Fix output statements in SimulatorFullyImplicitBlackoil::run().