Remove trivial affects generalization rules

[cbizon]

Summary

• Remove four AMIE rules where activity or abundance affects edges imply the broader activity_or_abundance affects edge.
• Prevent ARAGORN from synthesizing redundant inferred prediction edges when direct source edges already satisfy the broader query edge.
• Leave the remaining multi-edge AMIE rules unchanged.

Issue

The removed rules are logically true but trivial: the more specific qualifier set on the left-hand side already implies the broader activity_or_abundance qualifier set on the right-hand side. Underlying data-source edges with activity or abundance can be bound directly to an activity_or_abundance query edge, so Shepherd should not create an additional inferred edge supported only by those direct edges.

This fixes https://github.com/NCATSTranslator/Feedback/issues/1182.

Testing

• jq '[.[] | length] | add' workers/aragorn_lookup/rules_with_types_cleaned_finalized.json
• jq '[.. | objects | .Rule? // empty | select(. == "?a increased_activity_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b" or . == "?a increased_abundance_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b" or . == "?a decreased_activity_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b" or . == "?a decreased_abundance_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b")] | length' workers/aragorn_lookup/rules_with_types_cleaned_finalized.json
• uv run --with-requirements test-requirements.txt pytest tests/unit/aragorn/test_aragorn_lookup.py tests/unit/test_merge_message_helpers.py

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 56.45%. Comparing base (51c0931) to head (4d02146).
⚠️ Report is 12 commits behind head on main.
see 24 files with indirect coverage changes

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[maximusunc]

LGTM!