feat: Phase 5A — Engineering V1 foundation

First slice of the Engineering V1 sprint. Lays the schema + lifecycle
plumbing so the 10 canonical queries, memory graduation, and conflict
detection can land cleanly on top.

Schema (src/atocore/models/database.py):
- conflicts + conflict_members tables per conflict-model.md (with 5
  indexes on status/project/slot/members)
- memory_audit.entity_kind discriminator — same audit table serves
  both memories ("memory") and entities ("entity"); unified history
  without duplicating infrastructure
- memories.graduated_to_entity_id forward pointer for graduated
  memories (M → E transition preserves the memory as historical
  pointer)

Memory (src/atocore/memory/service.py):
- MEMORY_STATUSES gains "graduated" — memory-entity graduation flow
  ready to wire in Phase 5F

Engineering service (src/atocore/engineering/service.py):
- RELATIONSHIP_TYPES organized into 4 families per ontology-v1.md:
  + Structural: contains, part_of, interfaces_with
  + Intent: satisfies, constrained_by, affected_by_decision,
    based_on_assumption (new), supersedes
  + Validation: analyzed_by, validated_by, supports (new),
    conflicts_with (new), depends_on
  + Provenance: described_by, updated_by_session (new),
    evidenced_by (new), summarized_in (new)
- create_entity + create_relationship now call resolve_project_name()
  on write (canonicalization contract per doc)
- Both accept actor= parameter for audit provenance
- _audit_entity() helper uses shared memory_audit table with
  entity_kind="entity" — one observability layer for everything
- promote_entity / reject_entity_candidate / supersede_entity —
  mirror the memory lifecycle exactly (same pattern, same naming)
- get_entity_audit() reads from the shared table filtered by
  entity_kind

API (src/atocore/api/routes.py):
- POST /entities/{id}/promote (candidate → active)
- POST /entities/{id}/reject (candidate → invalid)
- GET /entities/{id}/audit (full history for one entity)
- POST /entities passes actor="api-http" through

Tests: 317 → 326 (9 new):
- test_entity_project_canonicalization (p04 → p04-gigabit)
- test_promote_entity_candidate_to_active
- test_reject_entity_candidate
- test_promote_active_entity_noop (only candidates promote)
- test_entity_audit_log_captures_lifecycle (before/after snapshots)
- test_new_relationship_types_available (6 new types present)
- test_conflicts_tables_exist
- test_memory_audit_has_entity_kind
- test_graduated_status_accepted

What's next (5B-5I, deferred): entity triage UI tab, core structure
queries, the 3 killer queries, memory graduation script, conflict
detection, MCP + context pack integration. See plan file.

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

src/atocore/models/database.py

@@ -136,6 +136,16 @@ def _apply_migrations(conn: sqlite3.Connection) -> None:
         "CREATE INDEX IF NOT EXISTS idx_memories_valid_until ON memories(valid_until)"
     )
 
+    # Phase 5 (Engineering V1): when a memory graduates to an entity, we
+    # keep the memory row as an immutable historical pointer. The forward
+    # pointer lets downstream code follow "what did this memory become?"
+    # without having to join through source_refs.
+    if not _column_exists(conn, "memories", "graduated_to_entity_id"):
+        conn.execute("ALTER TABLE memories ADD COLUMN graduated_to_entity_id TEXT")
+    conn.execute(
+        "CREATE INDEX IF NOT EXISTS idx_memories_graduated ON memories(graduated_to_entity_id)"
+    )
+
     # Phase 4 (Robustness V1): append-only audit log for memory mutations.
     # Every create/update/promote/reject/supersede/invalidate/reinforce/expire/
     # auto_promote writes one row here. before/after are JSON snapshots of the
@@ -160,6 +170,60 @@ def _apply_migrations(conn: sqlite3.Connection) -> None:
     conn.execute("CREATE INDEX IF NOT EXISTS idx_memory_audit_timestamp ON memory_audit(timestamp)")
     conn.execute("CREATE INDEX IF NOT EXISTS idx_memory_audit_action ON memory_audit(action)")
 
+    # Phase 5 (Engineering V1): entity_kind discriminator lets one audit
+    # table serve both memories AND entities. Default "memory" keeps existing
+    # rows correct; entity mutations write entity_kind="entity".
+    if not _column_exists(conn, "memory_audit", "entity_kind"):
+        conn.execute("ALTER TABLE memory_audit ADD COLUMN entity_kind TEXT DEFAULT 'memory'")
+    conn.execute(
+        "CREATE INDEX IF NOT EXISTS idx_memory_audit_entity_kind ON memory_audit(entity_kind)"
+    )
+
+    # Phase 5: conflicts + conflict_members tables per conflict-model.md.
+    # A conflict is "two or more active rows claiming the same slot with
+    # incompatible values". slot_kind + slot_key identify the logical slot
+    # (e.g., "component.material" for some component id). Members point
+    # back to the conflicting rows (memory or entity) with layer trust so
+    # resolution can pick the highest-trust winner.
+    conn.execute(
+        """
+        CREATE TABLE IF NOT EXISTS conflicts (
+            id TEXT PRIMARY KEY,
+            slot_kind TEXT NOT NULL,
+            slot_key TEXT NOT NULL,
+            project TEXT DEFAULT '',
+            status TEXT DEFAULT 'open',
+            resolution TEXT DEFAULT '',
+            resolved_at DATETIME,
+            detected_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+            note TEXT DEFAULT ''
+        )
+        """
+    )
+    conn.execute(
+        """
+        CREATE TABLE IF NOT EXISTS conflict_members (
+            id TEXT PRIMARY KEY,
+            conflict_id TEXT NOT NULL REFERENCES conflicts(id) ON DELETE CASCADE,
+            member_kind TEXT NOT NULL,
+            member_id TEXT NOT NULL,
+            member_layer_trust INTEGER DEFAULT 0,
+            value_snapshot TEXT DEFAULT ''
+        )
+        """
+    )
+    conn.execute("CREATE INDEX IF NOT EXISTS idx_conflicts_status ON conflicts(status)")
+    conn.execute("CREATE INDEX IF NOT EXISTS idx_conflicts_project ON conflicts(project)")
+    conn.execute(
+        "CREATE INDEX IF NOT EXISTS idx_conflicts_slot ON conflicts(slot_kind, slot_key)"
+    )
+    conn.execute(
+        "CREATE INDEX IF NOT EXISTS idx_conflict_members_conflict ON conflict_members(conflict_id)"
+    )
+    conn.execute(
+        "CREATE INDEX IF NOT EXISTS idx_conflict_members_member ON conflict_members(member_kind, member_id)"
+    )
+
     # Phase 9 Commit A: capture loop columns on the interactions table.
     # The original schema only carried prompt + project_id + a context_pack
     # JSON blob. To make interactions a real audit trail of what AtoCore fed