feat: Phase 5F/5G/5H — graduation, conflicts, MCP engineering tools

The population move + the safety net + the universal consumer hookup,
all shipped together. This is where the engineering graph becomes
genuinely useful against the real 262-memory corpus.

5F: Memory → Entity graduation (THE population move)
- src/atocore/engineering/_graduation_prompt.py: stdlib-only shared
  prompt module mirroring _llm_prompt.py pattern (container + host
  use same system prompt, no drift)
- scripts/graduate_memories.py: host-side batch driver that asks
  claude-p "does this memory describe a typed entity?" and creates
  entity candidates with source_refs pointing back to the memory
- promote_entity() now scans source_refs for memory:* prefix; if
  found, flips source memory to status='graduated' with
  graduated_to_entity_id forward pointer + writes memory_audit row
- GET /admin/graduation/stats exposes graduation rate for dashboard

5G: Sync conflict detection on entity promote
- src/atocore/engineering/conflicts.py: detect_conflicts_for_entity()
  runs on every active promote. V1 checks 3 slot kinds narrowly to
  avoid false positives:
  * component.material (multiple USES_MATERIAL edges)
  * component.part_of (multiple PART_OF edges)
  * requirement.name (duplicate active Requirements in same project)
- Conflicts + members persist via the tables built in 5A
- Fires a "warning" alert via Phase 4 framework
- Deduplicates: same (slot_kind, slot_key) won't get a new row
- resolve_conflict(action="dismiss|supersede_others|no_action"):
  supersede_others marks non-winner members as status='superseded'
- GET /admin/conflicts + POST /admin/conflicts/{id}/resolve

5H: MCP + context pack integration
- scripts/atocore_mcp.py: 7 new engineering tools exposed to every
  MCP-aware client (Claude Desktop, Claude Code, Cursor, Zed):
  * atocore_engineering_map (Q-001/004 system tree)
  * atocore_engineering_gaps (Q-006/009/011 killer queries — THE
    director's question surfaced as a built-in tool)
  * atocore_engineering_requirements_for_component (Q-005)
  * atocore_engineering_decisions (Q-008)
  * atocore_engineering_changes (Q-013 — reads entity audit log)
  * atocore_engineering_impact (Q-016 BFS downstream)
  * atocore_engineering_evidence (Q-017 inbound provenance)
- MCP tools total: 14 (7 memory/state/health + 7 engineering)
- context/builder.py _build_engineering_context now appends a compact
  gaps summary ("Gaps: N orphan reqs, M risky decisions, K unsupported
  claims") so every project-scoped LLM call sees "what we're missing"

Tests: 341 → 356 (15 new):
- 5F: graduation prompt parses positive/negative decisions, rejects
  unknown entity types, tolerates markdown fences; promote_entity
  marks source memory graduated with forward pointer; entity without
  memory refs promotes cleanly
- 5G: component.material + component.part_of + requirement.name
  conflicts detected; clean component triggers nothing; dedup works;
  supersede_others resolution marks losers; dismiss leaves both
  active; end-to-end promote triggers detection
- 5H: graduation user message includes project + type + content

No regressions across the 341 prior tests. The MCP server now answers
"which p05 requirements aren't satisfied?" directly from any Claude
session — no user prompt engineering, no context hacks.

Next to kick off from user: run graduation script on Dalidou to
populate the graph from 262 existing memories:
  ssh papa@dalidou 'cd /srv/storage/atocore/app && PYTHONPATH=src \
    python3 scripts/graduate_memories.py --project p05-interferometer --limit 30 --dry-run'

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

src/atocore/api/routes.py

@@ -1327,6 +1327,62 @@ def api_list_entities(
     }
 
 
+@router.get("/admin/conflicts")
+def api_list_conflicts(project: str | None = None) -> dict:
+    """Phase 5G: list open entity conflicts (optionally scoped to a project)."""
+    from atocore.engineering.conflicts import list_open_conflicts
+    conflicts = list_open_conflicts(project=project)
+    return {"conflicts": conflicts, "count": len(conflicts)}
+
+
+class ConflictResolveRequest(BaseModel):
+    action: str  # dismiss|supersede_others|no_action
+    winner_id: str | None = None
+
+
+@router.post("/admin/conflicts/{conflict_id}/resolve")
+def api_resolve_conflict(conflict_id: str, req: ConflictResolveRequest) -> dict:
+    """Resolve a conflict. Options: dismiss, supersede_others (needs winner_id), no_action."""
+    from atocore.engineering.conflicts import resolve_conflict
+    try:
+        success = resolve_conflict(
+            conflict_id=conflict_id,
+            action=req.action,
+            winner_id=req.winner_id,
+            actor="api-http",
+        )
+    except ValueError as e:
+        raise HTTPException(status_code=400, detail=str(e))
+    if not success:
+        raise HTTPException(status_code=404, detail=f"Conflict not found or already resolved: {conflict_id}")
+    return {"status": "resolved", "id": conflict_id, "action": req.action}
+
+
+@router.get("/admin/graduation/stats")
+def api_graduation_stats() -> dict:
+    """Phase 5F graduation stats for dashboard."""
+    from atocore.models.database import get_connection
+
+    with get_connection() as conn:
+        total_memories = int(conn.execute("SELECT COUNT(*) FROM memories WHERE status = 'active'").fetchone()[0])
+        graduated = int(conn.execute("SELECT COUNT(*) FROM memories WHERE status = 'graduated'").fetchone()[0])
+        entity_candidates_from_mem = int(conn.execute(
+            "SELECT COUNT(*) FROM entities WHERE status = 'candidate' "
+            "AND source_refs LIKE '%memory:%'"
+        ).fetchone()[0])
+        active_entities = int(conn.execute("SELECT COUNT(*) FROM entities WHERE status = 'active'").fetchone()[0])
+
+    return {
+        "active_memories": total_memories,
+        "graduated_memories": graduated,
+        "entity_candidates_from_memories": entity_candidates_from_mem,
+        "active_entities": active_entities,
+        "graduation_rate": (
+            graduated / (total_memories + graduated) if (total_memories + graduated) > 0 else 0.0
+        ),
+    }
+
+
 # --- Phase 5 Engineering V1: The 10 canonical queries ---