feat: cross-file entity links + Tier-3 entity questions

[v0ropaev]

Extends the entities extractor so a single entity artifact spans multiple files — the structural reason knowbase beats RAG — mirroring how the API extractor grounds a route on its handler + response_model across files. Also brings the Tier-3 A/B to a second knowledge type.

What

• entities.py (two-pass). Pass 1 classifies every class and indexes entities by short name; pass 2 resolves each entity's field-type references (list[LineItem], User | None, Mapped[list["Order"]]) and SQLAlchemy relationship() targets against that index, adding related_entity grounding edges (cross-file when the target lives elsewhere) + a related_entities payload. extractor_version 1 → 2 (derived-from set changes → ids rotate, gated per DESIGN §6; one-hop invalidation now links referenced→referencing entity). ForeignKey(...), transitive/aliased imports, association tables are documented gaps.
• embed/text.py. Enriched entity embed text (qualified name + field + related-entity names) so entity questions rank in search_knowledge.
• Tier-1 gate. Added a cross-file Cart → Order pair; test_cross_file_entity_links_grounded asserts the artifact is grounded on both files (role related_entity) and the reference resolves to shop.models.Order.
• Tier-3 A/B. A two-file Order/LineItem entity fixture + 3 entity questions; the harness indexes [FastAPIExtractor, EntityExtractor] and the generic recall loop asserts knowbase cross-file recall@5 == 1.0 for entity questions too (now 11 questions). RAG arm stays tracked/non-asserted.

Verification

• 52 eval tests pass; ruff + mypy --strict clean.
• Tier-3: knowbase cross-file recall@5 == 1.000 for all 11 questions; recall@1 separator knowbase 0.682 vs RAG 0.409.
• End-to-end on knowbase itself: 9/25 entities resolve links, incl. a genuine cross-file one — ExtractContext (base.py) → ParsedSpan (structural/interface.py); same-file links correctly add no extra file.

Store/queries unchanged (kind-opaque). Out of scope / documented follow-ups: ForeignKey("table.col") resolution, transitive imports, a separate entity_relation graph kind.