v0.4.0: Per-class annotation caps, TM-score length-normalization docs

Per-class annotation caps, TM-score length-normalization docs

protein_get_annotations gains a per-class limit; protein_compare_structures documents a TM-align sharp-edge.

Added:

• protein_get_annotations — limit input (1–200, default 50) caps features, natural variants, and InterPro domains independently; a capped or empty class is disclosed in the response notice, and truncated is set true when any class was capped. (#20)

Changed:

• protein_compare_structures — tool description and the tmScore output field document that TM-score is length-normalized and can shift sharply under terminal length differences; cross-check rmsd and alignedResidues. (#22)

266 tests pass; bun run devcheck clean.