feat: Engineering Knowledge Layer V1 — entities + relationships

Layer 2 of the AtoCore architecture. Adds typed engineering entities
with relationships on top of the flat memory/state/chunk substrate.

Schema:
- entities table: id, entity_type, name, project, description,
  properties (JSON), status, confidence, source_refs, timestamps
- relationships table: source_entity_id, target_entity_id,
  relationship_type, confidence, source_refs

15 entity types: project, system, subsystem, component, interface,
requirement, constraint, decision, material, parameter,
analysis_model, result, validation_claim, vendor, process

12 relationship types: contains, part_of, interfaces_with,
satisfies, constrained_by, affected_by_decision, analyzed_by,
validated_by, depends_on, uses_material, described_by, supersedes

Service layer: full CRUD + get_entity_with_context (returns an
entity with its relationships and all related entities in one call).

API endpoints:
- POST /entities — create entity
- GET /entities — list/filter by type, project, status, name
- GET /entities/{id} — entity + relationships + related entities
- POST /relationships — create relationship

Schema auto-initialized on app startup via init_engineering_schema().

7 tests covering entity CRUD, relationships, context traversal,
filtering, name search, and validation.

Test count: 290 -> 297.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/atocore/main.py

@@ -8,6 +8,7 @@ from atocore import __version__
 from atocore.api.routes import router
 import atocore.config as _config
 from atocore.context.project_state import init_project_state_schema
+from atocore.engineering.service import init_engineering_schema
 from atocore.ingestion.pipeline import get_source_status
 from atocore.models.database import init_db
 from atocore.observability.logger import get_logger, setup_logging
@@ -29,6 +30,7 @@ async def lifespan(app: FastAPI):
     _config.ensure_runtime_dirs()
     init_db()
     init_project_state_schema()
+    init_engineering_schema()
     log.info(
         "startup_ready",
         env=_config.settings.env,