Update Settings and main script

1) Changes to existing settings

Description	Motivation and Context
Added default value for `S.solver.run_as_batch_job` (false)	This was a required setting because it was used in main (i.e. before getDefaultSettings was called). This setting is now initialized to its default value in InitializeSettings
Changed default value for `S.OpenSimADOptions.verbose_mode` (false)	The verbose mode is only useful for debugging OpenSimAD errors.
Changed default value for `S.solver.CasADi_path` to use `casadi.GlobalOptions.getCasadiPath()`.	If casadi is on the matlab search path, you no longer have to pass it to this setting.
Move `save_folder` from subject to misc.	All other paths are in misc, so this is more consistent.
Move `savename` and `result_filename` from post_processing to misc.	All other file names are in misc, so this is more consistent.
Move `IG_selection` and `IG_selection_gaitCyclePercent` from subject to solver.	These relate to the solver, while subject settings are about tuning the neuromusculoskeletal model.
Changed `S.subject.v_pelvis_x_trgt` to `S.misc.forward_velocity`.	Task constraints (`gaitmotion_type`) are in misc. Changed name because: 1) we impose the velocity on the forward motion of the floating base, this does not have to be pelvis; 2) trgt (target) could mean that the velocity is in the objective ( $(v-v_{tgt})^2$ ), while this is not the case.
Renamed `S.weights.e_arm` to `S.weights.e_torqAct`.	This is the weight for the excitation of the torque actuators, which happen to drive the arms is the example models.
Removed `S.subject.spasticity` and `S.subject.muscle_coordination`.	These settings are not used.
Set `S.misc.main_path` in initializeSettings instead of in main.	Assigning this setting in main suggests the user can change its value, while it has to be the path to the PredSim repo.

2) New settings

Setting	Default	Motivation and Context
S.solver.constr_viol_tol_ipopt	6	Control the constraint violation tolerance independent of the convergence tolerance (tol_ipopt). Default chosen such that constraint violation at the solution is below 1E-6.
S.solver.nlpsol_options	`[]`	Makes it possible to pass options to CasADi's nlp solver.
S.solver.ipopt_options	`[]`	Makes it possible to pass options to ipopt.
S.weights.a_exp	2	Choose the exponent for the muscle activation term in the cost function.

3) Cleaner main script

Removed commented settings. A full overview of settings and defaults is in the readme. Having an overview for an arbitrary selection of settings in main might cause confusion.
Added some code to plot a figure, instead of calling run_this_file_to_plot_figures. Previously, running run_this_file_to_plot_figures multiple times could give problems because the array with results was not cleared between runs. If this script does not have to be called from main, we can always clear the array.
Moved
```
if S.solver.run_as_batch_job
add_pred_sim_to_batch(S,osim_path)
else
[savename] = run_pred_sim(S,osim_path);
end
```
To a new function, runPredSim. This way, users always call the same function, regardless of using batch jobs or not. This also avoids the possibility of calling add_pred_sim_to_batch with S.solver.run_as_batch_job = false (this could cause conflicts).

How Has This Been Tested?

Ran main script and compared result to example result.

Suggested tests for reviewers

Run main script.

To do

I will update the example results, to reflect the changes to the settings. I will do this after the changes to settings are approved.

KULeuvenNeuromechanics / PredSim

Update Settings and main script #144