v0.4.0

Multi-structure comparison (Slice D).

Added

• Pairwise RMSD matrix with sequence-aligned CA atoms by default
• Feature deltas vs reference (all numeric featurize fields; --delta-fields to narrow)
• CLI: compare <input> with JSON/CSV output to stdout or --out
• Reference modes: --reference, --auto-reference, --reference-by min|max:field, or first input
• Shared ligand/interface/quality flags from featurize
• Golden fixtures for compare regression tests

See CHANGELOG.md for full details.