Refactoring of simulation run script.

More script structure and simulation configuration now in a separate file
SimulationRunner extracted from main simulation running script.
Job starter edits - name changes and logic update

1) Function names are changed to use underscores instead of camelCase.
2) Now the run parameters are not stacked up but are replaced to run jobs correctly.
Simulation run checking script.

The script does the following things:
1) Checks if all jobs withing the given run are finished successfully.
2) If rerun flag set, reruns the jobs that failed with the same seed as previously.
Job id is replaced with the corresponding seed in the simulation output.
The folder with the output of a failed job is saved under the name:
{seed}_failed_{x}, where seed is the run seed and x is the next index of the failed run.