Introduce a Dedicated ConformationDAG Stage #362

Goal

Move conformational state construction out of the static LevelDAG node list and into a dedicated ConformationDAG stage, while preserving the current serial behaviour.

Background

The parent issue identifies conformational/dihedral analysis as trajectory-dependent work that currently runs as part of static setup. Before changing the algorithm, the workflow should first represent this as its own stage:

LevelDAG
  ├── StaticDAG
  ├── ConformationDAG
  └── FrameDAG / FrameScheduler

Scope

• Add a new ConformationDAG class.

• Update LevelDAG so the execution order becomes:

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

• Remove conformational state construction from the static DAG node list.

• Initially keep ConformationDAG as a wrapper around the existing ConformationStateBuilder.

• Preserve the existing output contract:

  • shared_data["conformational_states"]
  • shared_data["flexible_dihedrals"]

• Do not introduce chunking or Dask in this sub-issue.