Multiple updates to dymosim simulator:
  - Use a new subfolder for each simulation run
  - Number the results according to number of continuations
  - working_dir is no longer an argument (using the directory of the executable)
  - Finished documentation
  - Added a run log
  - dsres.mat, dsin.txt, and dsfinal.txt are automatically included in the results
  - Accepting nested dictionaries in params
  - Simulation options can be changed between runs
  - Create dsin file if it doesn't exist

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