Use identity-based set for collecting ontologies that may have the same ontology ID, when providing term labels to diffs.

[balhoff]

Resolves #1026.

• [ ] docs/ have been added/updated
• [x] tests have been added/updated
• [x] mvn verify says all tests pass
• [x] mvn site says all JavaDocs correct
• [x] CHANGELOG.md has been updated