feat(graph): close out Wave 7 — delete legacy + list_entities Protocol (W7-10)

Final close-out of Wave 7 §K.12: deletes the legacy
``aperag/domains/knowledge_graph/graphindex/`` package, drops the
legacy ``graphindex_*`` tables via alembic, and adds the one new
Protocol method (``LineageGraphStore.list_entities``) the architect
ratified to replace the legacy ``list_entities_for_curation`` /
``get_knowledge_graph`` enumerate-by-label paths the legacy package
owned.

This commit also folds in the grep-zero verification helper (formerly
PR #1763 by 冬柏) with ``_TASK10_LEGACY_DELETED`` flipped to True so the
10-pattern grep-zero contract becomes an active gate in this same PR
(architect-preferred atomic close-out, per simple-stable directive
#1 — fewer PRs, single CI run).

## Scope (per architect msg=28afe6ab + 4-question Q1-Q4 ratify msg=838d57c3 / msg=f3216dfc)

1. **NEW Protocol method ``LineageGraphStore.list_entities``**
   (``label / limit / offset`` kwargs) + ``EntityWithLineage`` rows
   sorted by ``name`` for deterministic pagination. InMemory
   reference + Postgres / Neo4j / Nebula production backends
   (mirror ``query_entities_by_keyword`` W6 #33 chunk 2 pattern).

2. **``aperag/domains/knowledge_graph/service.py:get_knowledge_graph``
   cutover** — 2-step pipeline replacing the legacy
   ``GraphIndexService.get_knowledge_graph``:

   1. ``store.list_entities(label, limit=query_max_nodes)`` —
      label-filtered entity list (primary work).
   2. ``GraphSearchService.get_subgraph(names, hops=max_depth)`` —
      optional edge expansion when ``max_depth > 0``.

   Each layer keeps clean semantics (W7-5 ``get_subgraph`` is
   anchor-expansion, not label-filter; using it as primary entry
   would force a wrapper that re-enumerated entities just to compute
   anchors — drift caught in architect own-up msg=838d57c3 → revise
   to ``list_entities`` primary).

3. **``CurationEntity`` adapter** (new
   ``aperag/graph_curation/dto.py``) replacing the legacy ``Entity``
   DTO. ``from_lineage(EntityWithLineage)`` constructor adapts the
   storage view into the shape ``build_candidate_pairs`` /
   ``_pair_score`` / ``_jaccard`` / ``entity_snapshot`` already
   accept — production-validated algorithm keeps its 0-signature
   change (architect Q2 ratify, simple-stable directive #3).

4. **``aperag/graph_curation/service.py`` cutover** —
   ``accept_suggestion`` and ``generate_run`` migrated off the
   legacy ``GraphIndexService`` bundle:

   - ``accept_suggestion`` delegates to
     ``LineageEntityMerger.merge_entities`` (W7-6, PR #1758) the same
     way the W7-8 ``GraphService.merge_entities`` route already does;
     both surfaces converge on a single merge path so user-merge-
     from-curation vs user-merge-from-graph-view never diverge.
   - ``generate_run`` signature now takes ``store`` /
     ``vector_connector`` / ``embedder`` / ``llm`` (architect Q3
     ratify) and uses two new helpers:
     - ``_enumerate_curation_entities`` — paged ``list_entities``
       loop adapting each row to ``CurationEntity``.
     - ``_fetch_shadow_neighbours`` — ANN search via
       ``VectorStoreConnector`` with the Wave 7 W7-3 3-field payload
       (``Eq("indexer", "graph_entity")`` filter) replacing the
       legacy ``find_entity_shadow_neighbors`` that filtered on the
       deleted ``entity_id`` payload field.

5. **``aperag/graph_curation/integration.py`` rewrite** —
   ``run_graph_curation_run_sync`` resolves the four Wave 7 deps
   via the same ``worker_factory`` factories the indexer / curation
   merger use, with a ``_SyncEmbedderShim`` adapter mirroring the
   one in ``worker_factory`` for the merge candidate detector.

6. **``build_collection_llm_callable`` relocation** — production
   call sites (``worker_factory._build_collection_graph_compactor``
   / ``_build_collection_summarizer``,
   ``aperag/graph_curation/lineage_merge.py:build_lineage_entity_merger_for``,
   ``aperag/graph_curation/integration.py``) all import from the
   canonical home ``aperag/indexing/llm.py`` (Q3 ratify; the file
   already exists, the legacy package was just re-exporting).

7. **Legacy package + tests deleted**:
   - ``aperag/domains/knowledge_graph/graphindex/`` (entire package)
   - ``tests/unit_test/graphindex/`` (entire dir)
   - ``tests/integration/compat/test_graph_compat.py`` (replaced
     by ``test_lineage_graph_compat.py`` in W7-1)

8. **Alembic drop migration** ``c7e3a1b9f4d6`` removes
   ``graphindex_chunks`` / ``graphindex_edges`` / ``graphindex_nodes``
   plus their indexes / unique constraints. Hard-cut policy per
   spec §K.12.12: legacy graph indexing was gated behind
   ``enable_knowledge_graph=False`` until Wave 4, then never wired
   into the new pipeline (``run_index_document_sync`` had 0
   production callers since Wave 4 hard-cut), so the tables are
   empty across every deployment. Downgrade recreates empty schema.

9. **Test rewrites** — three test files that consumed the legacy
   ``Entity`` DTO got updated:
   - ``tests/unit_test/graph_curation/test_service.py`` /
     ``test_candidate_generation.py`` — switched to
     ``CurationEntity as Entity``.
   - ``tests/unit_test/service/test_search_graph_contract.py`` —
     rewritten to consume ``EntityWithLineage`` /
     ``RelationWithLineage`` via the new
     ``_adapt_lineage_entities`` / ``_adapt_lineage_relations``
     adapters (the W7-1 lineage-side replacements for the deleted
     ``_adapt_nodes`` / ``_adapt_edges`` helpers).
   - 7 new InMemory ``list_entities`` unit tests in
     ``tests/unit_test/indexing/test_t1_2_graph.py`` covering
     empty-collection, sort, label filter, pagination,
     zero-or-negative limit, negative offset, compacted
     forward-compat.

## §K.12 invariant cross-check

| # | Invariant | This PR |
|---|-----------|---------|
| 1 | L1 graph data not polluted | ✅ ``list_entities`` is read-only; storage view → adapter projection only |
| 2 | L1 → L2 single-direction derive | ✅ no derived writes |
| 3 | Compactor before vector embed | N/A — read path |
| 4 | Vector store via Adaptor | ✅ ``_fetch_shadow_neighbours`` uses ``VectorStoreConnector`` only |
| 5 | payload indexer filter | ✅ ``Eq("indexer","graph_entity")`` filter; no legacy ``entity_id`` payload reference |
| 6 | uuid5 vector point id | N/A — read path |
| 7 | snapshot-diff lineage name set | N/A — read path |
| 8 | alias_map persist orphan | ✅ unaffected; alias_map is W7-6 owned |
| 9 | upsert_entity alias redirect | ✅ unaffected; decorator pattern preserved (curation flow uses inner store directly per architect msg=cf860ae4) |
| 10 | DB column length application-cap | ✅ no schema CHECK constraints introduced |
| 11 | candidate detection write-only | ✅ ``MergeCandidateDetector`` unchanged; ``generate_run`` uses same write boundary |
| 12 | grep-zero LightRAG | ✅ `rg "from aperag.domains.knowledge_graph.graphindex" aperag/ tests/` returns only the assertion in ``test_graph_search_migration.py:55``. ``rg "graphindex_*"`` against ``aperag/`` is 0 outside the alembic migration history. The 8 Wave 6-era ``# -- LightRAG-style query layer`` comments + W7-4 line 249 fallback + W7-5 docstrings remain (architect msg=3fe200be — they are descriptive comments referencing design heritage, removable in Wave 8 cleanup if desired) |

## 4-pattern pre-check matrix (paste from PR thread reply)

* **P1 v1** — ``rg "from aperag.domains.knowledge_graph.graphindex" aperag/ tests/`` produced 6 production / 11 import sites pre-PR; post-PR matches only ``test_graph_search_migration.py:55`` (the assertion-as-test that itself proves the migration is complete).
* **P1 v2** — every method on the legacy ``GraphIndexService`` that a non-legacy caller used is now accounted for: ``merge_entities`` → W7-8, ``get_knowledge_graph`` → 2-step pipeline above, ``list_entities_for_curation`` → ``LineageGraphStore.list_entities`` + ``CurationEntity.from_lineage``, ``find_entity_shadow_neighbors`` → ``_fetch_shadow_neighbours`` via ``VectorStoreConnector``, ``list_labels`` → already migrated W6 #40 + W7-1 ``compacted_description`` field.
* **P2** — alembic ``c7e3a1b9f4d6`` drops the legacy tables, alembic env.py loses the legacy ``graphindex.models`` import (replaced with explanatory comment); ``aperag_lineage_*`` tables stay intact.
* **P3** — single Protocol method addition (``list_entities``) — implemented across InMemory + 3 production backends + 7 unit tests.

## simple-stable 4-guardrail

| Guardrail | Status |
|---|---|
| #1 不无限扩范围 | ✅ ``list_entities`` is base capability mirroring `delete_entity` / `query_entities_by_keyword`; no new endpoints, no new schema tables |
| #2 尽快上线 | ✅ single PR closes Wave 7; all 11 prior task PRs already merged |
| #3 简单稳定 | ✅ adapter pattern preserves production-validated `build_candidate_pairs`; ``list_entities`` follows existing pagination idiom |
| #4 私有化部署免维护 | ✅ alembic auto-drops legacy tables; no operator config; ``list_entities`` uses the same backend factories the rest of Wave 7 wires |

## Test plan

- [x] All 1142 unit tests pass (``uv run pytest tests/unit_test/``)
- [x] ``alembic upgrade head --sql`` generates the expected
      ``DROP INDEX`` / ``DROP TABLE`` cascade
- [x] ``alembic heads`` resolves to single head ``c7e3a1b9f4d6``
- [x] ``ruff format --check`` / ``ruff check`` clean on touched files
- [ ] CI compat-graph + e2e-http stages — both gated post-merge
- [ ] Pair with 冬柏's grep-zero helper PR #1763 — flip
      ``_TASK10_LEGACY_DELETED=True`` once both PRs merge

Closes Wave 7. Next: architect final review per spec §K.12.12.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

## Fold-in: grep-zero verification helper (formerly PR #1763)

Per architect ratify + 冬柏 authorization, PR #1763 is folded into
this commit instead of shipping as a separate PR. Contents:

* **``tests/integration/test_w7_grep_zero_legacy_graphindex.py``**
  (NEW, 343 LOC) — 10 ripgrep contracts, one per legacy pattern,
  flipped to active gate (``_TASK10_LEGACY_DELETED = True``).
  Patterns cover:
  1. ``from aperag.domains.knowledge_graph.graphindex`` imports
  2. ``graphindex_(nodes|edges)`` table names (excludes the
     migration script itself)
  3. bare ``import aperag.domains.knowledge_graph.graphindex``
  4. ``_sync_entity_relation_vectors`` (W7-3 superseded)
  5. ``_compact_oversized_descriptions`` (W7-2 superseded)
  6. ``_summarize_description`` (W7-2 superseded)
  7. ``_fallback_truncate`` (renamed-and-kept on new
     ``GraphIndexCompactor`` — exception list documents the new home)
  8. ``_delete_removed_shadow_vectors`` (W7-3 superseded)
  9. ``GraphSearchContract.query_context`` (port name kept on the
     retrieval Protocol; legacy ``GraphIndexService.query_context``
     historical-context comments allow-listed)
  10. ``GraphIndexService.merge_entities`` (legacy class binding;
      historical-context comments in lineage_merge.py +
      test_wave7_task8_wiring.py allow-listed)
* **Self-exclusion**: ``_rg_count`` always excludes this helper file
  itself (every pattern is named in the docstring + assertion call
  site, which would otherwise self-trigger).
* **``aperag/mcp/server.py``** — bundled ruff-format/import-sort
  drift fix (post-#1762/#1759 leftover that pre-commit catches).
  Kept here so the close-out PR lands cleanly through ``make lint``.

## Test plan (final)

- [x] 1141 unit tests pass (``uv run pytest tests/unit_test/``)
- [x] 10/10 grep-zero integration tests pass
      (``uv run pytest tests/integration/test_w7_grep_zero_legacy_graphindex.py``)
- [x] ``alembic upgrade head --sql`` generates the expected
      ``DROP INDEX`` / ``DROP TABLE`` cascade
- [x] ``ruff format --check`` / ``ruff check`` clean on touched files
- [ ] CI e2e-http-smoke + e2e-http-provider — gated post-merge

Closes Wave 7. Next: architect final review per spec §K.12.12.

Co-Authored-By: 冬柏 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: earayu