Introduce Dedicated ConformationDAG Stage for Conformational Analysis

[harryswift01]

Summary

This PR introduces a dedicated ConformationDAG stage for conformational state construction. Previously, conformational/dihedral analysis was executed as part of the static LevelDAG node list. This change separates conformational state construction into its own workflow stage between static structural setup and frame-local covariance/neighbour execution, while preserving the existing serial ConformationStateBuilder behaviour.

Changes

Introduce ConformationDAG stage:

• Added a new ConformationDAG class to own conformational state construction.
• Kept the initial implementation as a wrapper around the existing ConformationStateBuilder.
• Preserved the existing conformational output contract:
  • shared_data["conformational_states"]
  • shared_data["flexible_dihedrals"]

Update LevelDAG orchestration:

Updated LevelDAG so workflow execution now follows:

1. static structural setup
2. conformational state construction
3. frame covariance/neighbour execution

• Removed conformational state construction from the static DAG node list.
• Added a dedicated _run_conformation_stage(...) method.
• Kept neighbour metadata initialisation and neighbour reduction around the frame stage.

Update tests and documentation:

• Replaced conformational static-node tests with ConformationDAG tests.
• Updated LevelDAG orchestration tests to include the new conformation stage.
• Removed autodoc references to the deleted conformational node module.
• Added API documentation for CodeEntropy.levels.conformation_dag.

Impact

• Makes the hierarchy-level workflow architecture clearer by separating static setup, conformational analysis, and frame-local execution.
• Keeps the current conformational algorithm and scientific output behaviour unchanged.
• Provides a dedicated stage boundary for future conformational map-reduce and Dask parallelisation work.
• Reduces the responsibility of the static DAG so it only handles structural setup.
• Keeps this change low-risk by preserving the existing serial ConformationStateBuilder implementation.

[jimboid]

This PR contains more work to pull out key code features so that we can build on the parallel code to bring more of the workload into the dask parallel segments of the program. Looks like everything has been included such as code, docs, tests etc and is a needed feature in the code base.