Improve examples based on JOSS review

[aguspesce]

To-do list to improve the examples based on the JOSS review:

• In run.sh use environmental variables.
  $ git grep /Users examples/continental_rift/run.sh:/Users/victorsacek/Documents/petsc/arch-label-debug/bin/mpirun -n 8 \ examples/continental_rift/run.sh:/Users/victorsacek/Documents/gits/md2d/md2d_aux/mandyoc \ examples/old_version/Crameri2012_Case2/run.sh:nohup /Users/victorsacek/Documents/petsc/arch-label-debug/bin/mpirun -n 4 ./mandyoc -denok 1.0e-15 -rtol 1.0e-7 -particles_per_ele 1000 -theta_FSSA 0.5 -sub_division_time_step 1.0 -visc_harmonic_mean 0 -particles_perturb_factor 0 -visc_const_per_element 1 -pressure_in_rheol 1 <FD.in >FD.out & examples/old_version/vanKeken1997/run.sh:nohup /Users/victorsacek/Documents/petsc/arch-label-debug/bin/mpirun -n 4 ./mandyoc -denok 1.0e-15 -particles_per_ele 1000 -theta_FSSA 0.5 -sub_division_time_step 1.0 -visc_harmonic_mean 0 -particles_perturb_factor 0 -visc_const_per_element 1 -pressure_in_rheol 1 <FD.in >FD.out & examples/old_version/vanKeken1997_nondim/run-mg.sh:nohup /Users/victorsacek/Documents/petsc/arch-label-debug/bin/mpirun -n 4 ./mandyoc -denok 1.0e-15 -particles_per_ele 1000 -theta_FSSA 0.5 -sub_division_time_step 1.0 -visc_harmonic_mean 0 -particles_perturb_factor 0 -visc_const_per_element 1 -direct_solver 0 -pressure_in_rheol 1 -veloc_ksp_monitor_true_residual -veloc_ksp_type fgmres -veloc_pc_type mg -veloc_pc_mg_galerkin -veloc_pc_mg_levels 3 -veloc_mg_levels_ksp_max_it 8 <FD.in >FD.out & examples/old_version/vanKeken1997_nondim/run.sh:nohup /Users/victorsacek/Documents/petsc/arch-label-debug/bin/mpirun -n 4 ./mandyoc -denok 1.0e-15 -particles_per_ele 1000 -theta_FSSA 0.5 -sub_division_time_step 1.0 -visc_harmonic_mean 0 -particles_perturb_factor 0 -visc_const_per_element 1 -direct_solver 0 -pressure_in_rheol 1 <FD.in >FD.out & examples/vanKeken1997_case1a/run.sh:/Users/kugelblitz/opt/petsc/arch-0-fast/bin/mpirun -n 2 /Users/kugelblitz/Desktop/mandyoc-misc/mandyoc/mandyoc

• Remove old_version folder.

• Maybe we can add a README file for each example, explaining the flag, how to run the example, and what each file is in the folder.

openjournals/joss-reviews#3551