protege-mcp v0.2.2

Closes the multi-module reconstruction gaps found by rebuilding the IOF ontology (iofoundry/ontology) through the tools alone. 41 → 47 tools.

New tools

• Structured SWRL rule editing — list_rules / add_rule / remove_rule read, add, and remove swrl:Imp axioms as structured body/head atoms (class, object_property, data_property, same_as, different_from, builtin). A ?-prefixed argument is a rule variable (?name → variable_namespace + name, ?<IRI> → that IRI exactly), so named variable IRIs like iof-var:process1 reconstruct faithfully where a ?x text syntax would lose them; rule-level annotations (rdfs:label/comment/…) ride the existing annotations operand. OWLAPI 4.5.29 ships no standalone SWRL parser, so the structured form is the round-trippable primitive.
• create_ontology — mint a new empty module in the workspace and make it the active edit target (pairs with set_ontology_id), so a multi-module ontology can be built from nothing.
• write_catalog — generate/refresh an OASIS catalog-v001.xml mapping the active ontology's imports (ontology + version IRIs) to their local files, so a reconstructed module re-opens in Protégé with imports resolved offline. Catalog files live outside the OWL axiom model, so no other tool can produce them.
• diff_ontologies — axiom-level semantic diff / round-trip check between two loaded ontologies, or the active ontology against a freshly-loaded document (without adding it to the workspace); identical=true means the reconstruction is axiom-for-axiom faithful.

Notes

• OWLAPI stays at 4.5.29 (provided by Protégé 5.6.6 and shared with the live OWLModelManager); these tools need nothing newer.
• Requires a Java 17+ JVM (unchanged).

Install: download protege-mcp-0.2.2.jar below, or use Protégé ▸ File ▸ Check for plugins.