update reference values

...s/GursonPlasticInstabilities_PathFollowing/Plane_notch.py

...nThomasonMultipleNonlocalVar_PathFollowing/Plane_notch.py

.../benchmarks/GursonThomason_cube_I1J2J3_Transition/cube.py

dG3D/benchmarks/GursonThomason_cube_Transition/cube.py

dG3D/benchmarks/GursonThomason_cube_withLodeEnhanced/cube.py

dG3D/benchmarks/Inno_EMT_test/InnoElecMagTherm.py

dG3D/benchmarks/defoDefoContactSlaveEdge2DQuad/squares.py

.../benchmarks/defoDefoContactSlaveEdge2DQuadPert/squares.py

dG3D/benchmarks/linearEMT/LinearElecMagTherm.py

dG3D/benchmarks/linearEMT_Pert/LinearElecMagTherm_Pert.py

dG3D/benchmarks/linearElectroMagnetic/LinearElecMag.py

...marks/multiscale_2order_shearlayer_pert/shearlayerPert.py

dG3D/benchmarks/nanoIndentation/ni.py

dG3D/benchmarks/shiftMultiSystem/run.py

dG3D/benchmarks/torchUniaxial/energy.csv

dG3D/benchmarks/torchUniaxial/macro_cpp.py