logs: migrate to molecular CoT JSON protocol, fix regressions

- Replace BeliefFormatter with CotJsonFormatter (single-line JSON with
  ts, level, trace_id, src, marker, intent, payload, error, span_id)
- Migrate belief_scope to use cot_log() for structured JSON output
- Update monkey-patched reason/reflect/explore to pass extra= dict
- Strip 200+ inline [REASON]/[REFLECT]/[EXPLORE] markers from 50+ files
- Remove belief_scope from hot-path utilities (_parse_datetime,
  _json_load_if_needed) to eliminate startup log noise
- Register TraceContextMiddleware in app.py (was implemented but unused)
- Seed trace_id in startup_event/shutdown_event for background tasks
- Fix broken relative imports in translate routes (3 dots → 4 dots)
- Migrate 43 translate_routes log calls to logger.reason/explore
- Fix SyntaxError (positional arg after extra=) in _repo_operations_routes
- Fix IndentationError in rbac_permission_catalog except-block
- Add smoke test tests/test_smoke_app.py (catches import errors before run)

backend/src/scripts/migrate_sqlite_to_postgres.py

@@ -164,8 +164,9 @@ def _ensure_target_schema(engine) -> None:
 def _migrate_config(engine, legacy_config_path: Optional[Path]) -> int:
     with belief_scope("_migrate_config"):
         if legacy_config_path is None:
-            logger.info(
-                "[_migrate_config][REASON] No legacy config.json found, skipping"
+            logger.reason(
+                "No legacy config.json found, skipping",
+                extra={"src": "_migrate_config"},
             )
             return 0
 
@@ -327,8 +328,9 @@ def run_migration(
     sqlite_path: Path, target_url: str, legacy_config_path: Optional[Path]
 ) -> Dict[str, int]:
     with belief_scope("run_migration"):
-        logger.info(
-            "[run_migration][REASON] sqlite=%s target=%s", sqlite_path, target_url
+        logger.reason(
+            f"sqlite={sqlite_path} target={target_url}",
+            extra={"src": "run_migration"},
         )
         if not sqlite_path.exists():
             raise FileNotFoundError(f"SQLite source not found: {sqlite_path}")

backend/src/scripts/seed_superset_load_test.py

@@ -157,8 +157,9 @@ def _resolve_target_envs(env_ids: List[str]) -> Dict[str, Environment]:
                     env = Environment(**row)
                     configured[env.id] = env
             except Exception as exc:
-                logger.warning(
-                    f"[REFLECT] Failed loading environments from {config_path}: {exc}"
+                logger.reflect(
+                    f"Failed loading environments from {config_path}: {exc}",
+                    extra={"src": "_resolve_target_envs"},
                 )
 
     for env_id in env_ids:
@@ -271,8 +272,9 @@ def seed_superset_load_data(args: argparse.Namespace) -> Dict:
         templates_by_env[env_id] = _build_chart_template_pool(
             client, args.template_pool_size, rng
         )
-        logger.info(
-            f"[REASON] Environment {env_id}: loaded {len(templates_by_env[env_id])} chart templates"
+        logger.reason(
+            f"Environment {env_id}: loaded {len(templates_by_env[env_id])} chart templates",
+            extra={"src": "seed_superset_load_data"},
         )
 
     errors = 0
@@ -285,8 +287,9 @@ def seed_superset_load_data(args: argparse.Namespace) -> Dict:
         dashboard_title = _generate_unique_name("lt_dash", used_dashboard_names, rng)
 
         if args.dry_run:
-            logger.info(
-                f"[REFLECT] Dry-run dashboard create: env={env_id}, title={dashboard_title}"
+            logger.reflect(
+                f"Dry-run dashboard create: env={env_id}, title={dashboard_title}",
+                extra={"src": "seed_superset_load_data"},
             )
             continue
 
@@ -301,7 +304,7 @@ def seed_superset_load_data(args: argparse.Namespace) -> Dict:
             created_dashboards[env_id].append(dashboard_id)
         except Exception as exc:
             errors += 1
-            logger.error(f"[EXPLORE] Failed creating dashboard in {env_id}: {exc}")
+            logger.explore(f"Failed creating dashboard in {env_id}: {exc}", extra={"src": "seed_superset_load_data"})
             if errors >= args.max_errors:
                 raise RuntimeError(
                     f"Stopping due to max errors reached ({errors})"
@@ -351,10 +354,10 @@ def seed_superset_load_data(args: argparse.Namespace) -> Dict:
             created_charts[env_id].append(chart_id)
 
             if (index + 1) % 500 == 0:
-                logger.info(f"[REASON] Created {index + 1}/{args.charts} charts")
+                logger.reason(f"Created {index + 1}/{args.charts} charts", extra={"src": "seed_superset_load_data"})
         except Exception as exc:
             errors += 1
-            logger.error(f"[EXPLORE] Failed creating chart in {env_id}: {exc}")
+            logger.explore(f"Failed creating chart in {env_id}: {exc}", extra={"src": "seed_superset_load_data"})
             if errors >= args.max_errors:
                 raise RuntimeError(
                     f"Stopping due to max errors reached ({errors})"
@@ -381,8 +384,9 @@ def main() -> None:
     with belief_scope("seed_superset_load_test.main"):
         args = _parse_args()
         result = seed_superset_load_data(args)
-        logger.info(
-            f"[REFLECT] Result summary: {json.dumps(result, ensure_ascii=True)}"
+        logger.reflect(
+            f"Result summary: {json.dumps(result, ensure_ascii=True)}",
+            extra={"src": "main"},
         )