feat(config): persist config.patch updates atomically

docs/plans/state.json

@@ -2524,6 +2524,29 @@
         "docs/plans/analysis/2026-02-16-codebase-audit-report.md"
       ],
       "test_status": "pnpm test:run src/models/router.test.ts + pnpm typecheck passing"
+    },
+    "audit-followup-config-patch-persistence": {
+      "status": "completed",
+      "date": "2026-02-16",
+      "updated": "2026-02-16",
+      "summary": "Implemented durable config.patch persistence when config path is known: patches are applied to a draft, atomically written to disk with .bak backup, then committed to runtime config only on successful persist. Added persisted/persistError response fields and settings UI messaging for runtime-only saves.",
+      "files_created": [
+        "src/config/persistence.ts",
+        "src/config/persistence.test.ts"
+      ],
+      "files_modified": [
+        "src/config/index.ts",
+        "src/gateway/handlers/config.ts",
+        "src/gateway/handlers/handlers.test.ts",
+        "src/gateway/server.ts",
+        "src/daemon/services.ts",
+        "src/daemon/index.ts",
+        "src/cli/start.ts",
+        "src/cli/setup.ts",
+        "src/gateway/ui/pages/settings.js",
+        "docs/plans/analysis/2026-02-16-codebase-audit-report.md"
+      ],
+      "test_status": "pnpm test:run src/gateway/handlers/handlers.test.ts src/config/persistence.test.ts + pnpm typecheck passing"
     }
   },
   "overall_progress": {