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/api/routes/settings.py

@@ -88,7 +88,7 @@ async def get_settings(
     _=Depends(has_permission("admin:settings", "READ")),
 ):
     with belief_scope("get_settings"):
-        logger.info("[get_settings][REASON] Fetching all settings")
+        logger.reason("Fetching all settings", extra={"src": "get_settings"})
     config = config_manager.get_config().copy(deep=True)
     config.settings.llm = normalize_llm_settings(config.settings.llm)
     # Mask passwords
@@ -127,7 +127,7 @@ async def update_global_settings(
     _=Depends(has_permission("admin:settings", "WRITE")),
 ):
     with belief_scope("update_global_settings"):
-        logger.info("[update_global_settings][REASON] Updating global settings")
+        logger.reason("Updating global settings", extra={"src": "update_global_settings"})
 
     config_manager.update_global_settings(settings)
     return settings
@@ -183,7 +183,7 @@ async def get_environments(
     _=Depends(has_permission("admin:settings", "READ")),
 ):
     with belief_scope("get_environments"):
-        logger.info("[get_environments][REASON] Fetching environments")
+        logger.reason("Fetching environments", extra={"src": "get_environments"})
     environments = config_manager.get_environments()
     return [
         env.copy(update={"url": _normalize_superset_env_url(env.url)})
@@ -205,7 +205,7 @@ async def add_environment(
     _=Depends(has_permission("admin:settings", "WRITE")),
 ):
     with belief_scope("add_environment"):
-        logger.info(f"[add_environment][REASON] Adding environment {env.id}")
+        logger.reason(f"Adding environment {env.id}", extra={"src": "add_environment"})
     env = env.copy(update={"url": _normalize_superset_env_url(env.url)})
 
     # Validate connection before adding (fast path)
@@ -237,7 +237,7 @@ async def update_environment(
     config_manager: ConfigManager = Depends(get_config_manager),
 ):
     with belief_scope("update_environment"):
-        logger.info(f"[update_environment][REASON] Updating environment {id}")
+        logger.reason(f"Updating environment {id}", extra={"src": "update_environment"})
 
     env = env.copy(update={"url": _normalize_superset_env_url(env.url)})
 
@@ -278,7 +278,7 @@ async def delete_environment(
     id: str, config_manager: ConfigManager = Depends(get_config_manager)
 ):
     with belief_scope("delete_environment"):
-        logger.info(f"[delete_environment][REASON] Deleting environment {id}")
+        logger.reason(f"Deleting environment {id}", extra={"src": "delete_environment"})
     config_manager.delete_environment(id)
     return {"message": f"Environment {id} deleted"}
 
@@ -295,7 +295,7 @@ async def test_environment_connection(
     id: str, config_manager: ConfigManager = Depends(get_config_manager)
 ):
     with belief_scope("test_environment_connection"):
-        logger.info(f"[test_environment_connection][REASON] Testing environment {id}")
+        logger.reason(f"Testing environment {id}", extra={"src": "test_environment_connection"})
 
     # Find environment
     env = next((e for e in config_manager.get_environments() if e.id == id), None)
@@ -351,8 +351,8 @@ async def update_logging_config(
     _=Depends(has_permission("admin:settings", "WRITE")),
 ):
     with belief_scope("update_logging_config"):
-        logger.info(
-            f"[update_logging_config][REASON] Updating logging config: level={config.level}, task_log_level={config.task_log_level}"
+        logger.reason(
+            f"Updating logging config: level={config.level}, task_log_level={config.task_log_level}", extra={"src": "update_logging_config"}
         )
 
         # Get current settings and update logging config
@@ -475,8 +475,8 @@ async def update_consolidated_settings(
     _=Depends(has_permission("admin:settings", "WRITE")),
 ):
     with belief_scope("update_consolidated_settings"):
-        logger.info(
-            "[update_consolidated_settings][REASON] Applying consolidated settings patch"
+        logger.reason(
+            "Applying consolidated settings patch", extra={"src": "update_consolidated_settings"}
         )
 
         current_config = config_manager.get_config()