fix(main): replace electron-store with native fs for ESM compatibility

- Remove electron-store dependency usage (ESM-only)
- Implement JSON file storage using native fs module
- Read/write config.json and secure.json directly
- Maintain same API for domain and version storage

.sisyphus/boulder.json

@@ -6,6 +6,11 @@
   "agent": "atlas",
   "worktree_path": "C:\\dev\\workspace\\kintone\\kintone-customize-manager",
   "progress": {
+    "completed_waves": 6,
+    "total_waves": 6,
+    "status": "completed",
+    "last_updated": "2026-03-12T02:00:00.000Z"
+  }
     "completed_waves": 4,
     "total_waves": 6,
     "status": "in_progress",