remove relationships with phantom entities

[dayesouza]

This pull request introduces a new utility for filtering out "phantom" or orphaned relationships in graph extraction and update workflows. It ensures that relationships whose source or target entities do not exist are removed, preventing downstream errors caused by hallucinated or broken graph edges. The change is applied in both the graph extraction and incremental update pipelines, and is thoroughly tested with new unit tests.

Graph extraction and update pipeline improvements:

• Added the filter_orphan_relationships utility function in utils.py, which removes relationships referencing non-existent entities after LLM graph extraction. This prevents phantom edges in the graph and logs warnings when such relationships are dropped.
• Integrated filter_orphan_relationships into the graph extraction workflow (extract_graph.py) and the incremental update workflow (update_entities_relationships.py), ensuring orphan relationships are filtered out in both initial and update passes. [1] [2] [3] [4]

Testing and validation:

• Added comprehensive unit tests for filter_orphan_relationships, _merge_entities, and _merge_relationships in test_extract_graph.py, covering edge cases such as missing sources/targets, empty inputs, and index resetting.
• Added unit tests for orphan filtering in the update pipeline in test_update_relationships.py, validating that merged relationships with hallucinated endpoints are correctly removed after entity/relationship updates.
• Added missing copyright headers to test files.

Release and documentation:

• Documented this feature as a patch update in .semversioner/next-release/patch-20260302221432185149.json.