Update code comments and typespecs across modules

Enhanced overall code clarity by adding and revising detailed comments, docstrings, and typespecs in various Python modules. Significant changes include refining functionality of effect management in 'effects.py', modifications to use of 'numpy' arrays and functions in 'movement.py', as well as adjustments to handling hooks. Additionally, minor updates in 'configs/study/level1/level1_config.yaml' and 'counter_factory.py' were made.