Tidy level package structure

[harryswift01]

Summary

This PR tidies the levels package structure by moving level-stage DAG orchestration files into a dedicated levels.graph package. It also updates imports and documentation generation so the new module paths are used consistently.

Changes

Move level DAG orchestration into levels.graph:

• Moved conformation_dag.py, frame_dag.py, and level_dag.py into CodeEntropy.levels.graph.
• Kept the DAG implementation unchanged apart from import-path updates.

Refresh API documentation:

• Regenerated the Sphinx API documentation for the updated package layout.
• Removed stale references to the old CodeEntropy.levels.frame_dag, CodeEntropy.levels.level_dag, and CodeEntropy.levels.conformation_dag module paths.
• Updated the generated API docs so the new CodeEntropy.levels.graph modules are documented correctly.

Impact

• Makes the levels package easier to navigate by separating DAG orchestration from calculation utilities and DAG nodes.
• Reduces top-level clutter in CodeEntropy.levels.
• Does not change runtime behaviour or scientific outputs.
• Keeps documentation aligned with the new package structure.

[jimboid]

Mostly tidying and import chores.