materialize OVERRIDES rel and bump ontology to 13

[HumanBean17]

Summary

• Implements PR-A from plans/PLAN-HINTS.md (stored [:OVERRIDES] edges, ONTOLOGY_VERSION 13, EdgeType + neighbors + tests + README). Background: propose/HINTS-ROAD-SIGNS-PROPOSE.md §6 / §7.17.
• Materializes (subtype_method)-[:OVERRIDES]->(supertype_declared_method) in build_ast_graph.py (one IMPLEMENTS/EXTENDS hop, matching signature, deduped + deterministic order). Schema drop/create wired; counts_json includes overrides.
• Bumps ast_java.ONTOLOGY_VERSION to 13; extends kuzu_queries._EDGE_TYPES so meta() edge counts include OVERRIDES.
• Adds OVERRIDES to mcp_v2.EdgeType, updates NodeRecord.edge_summary and server tool copy so stored OVERRIDES is valid in neighbors; virtual keys unchanged.
• README: ontology 13, re-index callout, graph edge table (10 types).
• Tests: all six PR-A names in tests/test_mcp_v2_compose.py, plus schema / MCP enum updates.
• Docs follow-up: AGENTS.md, docs/AGENT-GUIDE.md, .cursor/rules/*, CODEBASE_REQUIREMENTS.md now reference ontology 13 and the OVERRIDES / neighbors story.

Re-index / ontology

Ontology 13 — full graph rebuild required (java-codebase-rag reprocess default or build_ast_graph.py); indexes built before this version are below KuzuGraph’s required ontology check.

Manual evidence

rm -rf /tmp/hints-pr-a && mkdir -p /tmp/hints-pr-a && \
  .venv/bin/python build_ast_graph.py \
  --source-root tests/fixtures/override_axis_rollup_smoke \
  --kuzu-path /tmp/hints-pr-a/code_graph.kuzu
.venv/bin/python -c "import kuzu; c=kuzu.Connection(kuzu.Database('/tmp/hints-pr-a/code_graph.kuzu',read_only=True)); r=c.execute('MATCH ()-[e:OVERRIDES]->() RETURN count(e) AS n'); print('OVERRIDES count:', int(r.get_next()[0]) if r.has_next() else 0)"

Expected: OVERRIDES count: 3 on that fixture.

Test plan

• .venv/bin/ruff check .
• PATH="<repo>/.venv/bin:$PATH" .venv/bin/python -m pytest tests -v (457 passed, 10 skipped; CLI subprocess tests need venv-first PATH on hosts that shadow java-codebase-rag)

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