Seems like this merge-axiom-annotations option was being ignored.
@@ -109,8 +109,10 @@ public class RepairOperation {
Set<InvalidReferenceViolation> violations =
InvalidReferenceChecker.getInvalidReferenceViolations(ontology, true);
repairInvalidReferences(ioHelper, ontology, violations, migrateAnnotations);
+ if (mergeAxiomAnnotations) {
mergeAxiomAnnotations(ontology);
}
+ }
/**
* Given an ontology, merge the annotations of duplicate axioms to create one axiom with all
