Live smoke test (Protégé + MCP)

The unit tests (mvn test) cover the tool cores in isolation, and ToolPipelineTest chains them end-to-end headlessly (load → edit → validate → govern → diff → SPARQL) so a cross-tool regression fails in CI. What they cannot cover is the live stack: the OSGi bundle loading in a real Protégé, the HTTP/OAuth transport, the EDT marshalling, and a real reasoner. This checklist is the manual counterpart — run it against the built v0.3.3 jar before publishing a release.

Setup

1. mvn clean package and copy target/protege-mcp-0.3.3.jar into /Applications/Protégé.app/Contents/plugins/ (replace the older versioned jar — keep exactly one).
2. Launch Protégé on a Java 17+ JVM (PROTEGE_JAVA_HOME), open the MCP Server view, and Start the server. Note the bound URL and bearer token.
3. Point an MCP client at it (e.g. tools/chat-repro.sh "$(pbpaste)" "…" "http://127.0.0.1:8123/mcp", or the in-app Ontology Assistant tab).

Flow (each step should return structured JSON, no error, and be visible in the GUI)

#	Tool call	Expect
1	load_ontology a real ontology (e.g. an IOF module)	becomes the active ontology; imports resolved
2	get_ontology_context	signature counts, imports, prefixes, reasoner state
3	create_term name=SmokeTestThing, parent=owl:Thing, definition=…	one entity + label + definition + parent, one undo entry
4	create_property name=smokeRelatesTo, domain/range/characteristics	one property with its axioms, one undo entry
5	move_class the new term under a different parent	named parent replaced; subtree intact
6	validate_ontology	modelling-quality report; new term clean
7	validate_governance owl_profile=DL, required_annotations=[label, definition]	profile verdict + governance findings; UI stays responsive on a large closure (profile check runs off-EDT)
8	run_reasoner then get_inferred_superclasses	classifies; inferred relations returned
9	get_explanations for a property-hierarchy entailment	falls back to entailed=true + related_axioms (structural context), not an error
10	sparql_query a SELECT touching the new term	the new term appears in the results
11	save_ontology then diff_ontologies against the saved document	identical=true
12	undo_change ×N / redo_change	each macro reverts as a single step
13	deprecate_entity the new term, replaced_by another	owl:deprecated true + replaced-by pointer in the GUI

Any step that errors, freezes the UI, or does not appear in Protégé’s editor/undo stack is a release blocker — capture the JSON error and the Protégé log.