Refactor timestep entropy computation workflow into modular, maintainable components:

- Extracted dihedral conformation logic into a new helper method.
- Modularized the `_compute_entropies` method to delegate level-specific logic cleanly, including:
 - United atom level: per-residue dihedral state assignment and entropy processing.
 - Residue level: molecule-wide dihedral state assignment and entropy processing.
 - Polymer level: vibrational entropy only.
- Introduced `_initialize_molecules`, `_build_covariance_matrices`, and `_update_force_torque_matrices` to encapsulate setup logic and matrix construction.
- Implemented `_handle_water_entropy` to isolate water-specific entropy logic and update selection strings accordingly.
- Ensured all new methods follow consistent naming and parameter conventions.

Author: harryswift01