feat(transformation): z-sorting threshold via YAML config

[webdevred]

• Added TransformationConfig type with FromJSON instance in Types.hs.
• Introduced new Config module to load z-sorting-threshold from transformation.yaml (defaults to 0.05).
• Threaded Scientific threshold through transformation pipeline (transform, updateVertexForest, sortVertices, etc.).
• Replaced fixed sortOn with threshold-aware sortBy logic in sortCommentGroups.
• Updated Main to call loadThreshold and pass value into applyTransform.
• Added yaml dependency to package.yaml.