mirpy 4.7.0

Add mir.embedding.reference.build_reference_rotations for separate PCA outputs over raw vdjtools features and sample RFF embeddings. Save up to 1024 sample PCs with explained-variance ratios, and reuse matching RFF basis files unchanged for PCA-only refits.

The documentation explains reference selection, coordinate compatibility, saved-model checks and applying rotations. Sample embedding remains clonotype embedding → shared RFF → weighted sample mean → optional sample PCA. Existing signatures are unchanged. Fitted PCA bundles remain separate outputs and are excluded from package distributions and release assets.

Requires vdjtools>=5.1.0, verified on public PyPI before integration. All five release-head CI jobs passed, including optional Torch/ANN/BioPython/Parquet and bounded cohort resource checks. Focused tests, warning-free documentation, distribution inventory checks and isolated paired installation/PCA compatibility passed.