Resolved merge conflicts with renamed and deleted files

.DS_Store

ref/.DS_Store

ref/archive/.DS_Store

ref/archive/geant4_simulation/.DS_Store

...ant4_simulation/.ipynb_checkpoints/__init__-checkpoint.py

...eant4_simulation/.ipynb_checkpoints/actions-checkpoint.py

...nt4_simulation/.ipynb_checkpoints/materials-checkpoint.py

...nt4_simulation/.ipynb_checkpoints/vis_dawn-checkpoint.mac

ref/archive/geant4_simulation/__init__.py

...ve/geant4_simulation/__pycache__/__init__.cpython-311.pyc

...ive/geant4_simulation/__pycache__/__init__.cpython-39.pyc

...hive/geant4_simulation/__pycache__/actions.cpython-39.pyc

...ve/geant4_simulation/__pycache__/materials.cpython-39.pyc

ref/archive/geant4_simulation/__pycache__/vis.cpython-39.pyc

ref/archive/geant4_simulation/actions.py

ref/archive/geant4_simulation/geometry/.DS_Store

...imulation/geometry/.ipynb_checkpoints/EMCal-checkpoint.py

...lation/geometry/.ipynb_checkpoints/__init__-checkpoint.py

...eometry/.ipynb_checkpoints/example_geometry-checkpoint.py

...imulation/geometry/.ipynb_checkpoints/pbbox-checkpoint.py