protege-mcp v0.2.1

protege-mcp 0.2.1 — tool-driven construction ergonomics

Driving a real BFO/IOF ontology (IOF Biopharma/Agent) entirely through the tools surfaced the friction points of natural-language-driven authoring. This release closes them. Additive and backward-compatible; 37 → 41 tools.

• set_active_ontology — switch which loaded ontology your edits target. load_ontology keep_active=true and add_import document=… now resolve imports without stealing the active ontology (the #1 wall in the reconstruction).
• apply_changes — apply a previewed operations[] batch in one call and one undo entry (a single undo_change reverts the whole batch, like create_class). Reports per-operation results, the new entities each add introduces, and a summary. strict=true skips any add that would mint a brand-new entity from an unrecognized IRI/name.
• set_label — upsert an rdfs:label (removes the same-language label, adds the new one). set_prefix — register/update a prefix in the active ontology's format.
• Silent-minting signal — every write tool (add_axiom, add_subclass_of, add_annotation, apply_changes) now reports the entities a change introduces, with an opt-in strict flag that refuses to fabricate one from a typo'd IRI/name.
• create_class / create_entity gain namespace (mint the IRI in a shared namespace distinct from the ontology IRI), plus label / label_lang / no_label for language-tagged or suppressed labels — no more stray untagged xsd:string labels.
• Manchester <IRI> operands now resolve inside compound class expressions (e.g. <…/Identifier> and (…)).
• Richer reads & checks — validate_ontology with_reasoner=true adds a consistency / unsatisfiable-class verdict; get_entity_context neighbours are structured {iri, display, type}; undo_change / redo_change report the axiom delta.

Requires Java 17. Install via Protégé ▸ File ▸ Check for plugins, or drop protege-mcp-0.2.1.jar into the Protégé plugins/ directory and restart.