Updating Sphinx documentation and typing for PyRosettaCluster

[klimaj]

This PR adds several improvements to the PyRosettaCluster framework (to be merged after #636 for incremental versioning).

Major changes (maintaining runtime functionality)

1. Improve formatting and clarity of docstrings for Sphinx-based PyRosetta documentation.
2. Consolidate typing aliases into a single pyrosetta.distributed.cluster.type_defs module for easier maintainability.
3. Add typing to attributes in attrs classes.
4. Clean up imports and typing (preserving Python-3.8 compatibility)
5. Add pickle and cloudpickle warnings to relevant docstrings.
6. Clarify and format logging and error messages.
7. Add PackedPoseHasher and secure_read_pickle to the top-level pyrosetta.distributed.cluster namespace for easier usability.

Minor changes (updating runtime functionality)

8. Update usage of dataclasses module to use the attrs package instead. Also package Dask task arguments in a new ExtraArgs attrs class (with slots and typing) instead of a simple dictionary.
9. Slightly loosen a validation: test whether two Base64-encoded pickled Pose objects are identical -> test whether the scientific state of two Pose objects are identical.
10. Handle edge case of single dictionary outputs from PyRosetta protocols decorated with the reserve_scores decorator.
11. Handle edge case of unordered iterables (i.e., set objects) and raise exceptions: input PyRosetta protocols, and outputs produced by PyRosetta protocols, must be ordered for reproducibility purposes.
12. Fix exception handling for Exception rather than BaseException.