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/core/database.py

@@ -156,9 +156,9 @@ def _ensure_user_dashboard_preferences_columns(bind_engine):
                 for statement in alter_statements:
                     connection.execute(text(statement))
         except Exception as migration_error:
-            logger.warning(
-                "[database][EXPLORE] Profile preference additive migration failed: %s",
-                migration_error,
+            logger.explore(
+                "Profile preference additive migration failed",
+                extra={"src": "database", "error": str(migration_error)},
             )
 
 
@@ -202,9 +202,9 @@ def _ensure_user_dashboard_preferences_health_columns(bind_engine):
                 for statement in alter_statements:
                     connection.execute(text(statement))
         except Exception as migration_error:
-            logger.warning(
-                "[database][EXPLORE] Profile health preference additive migration failed: %s",
-                migration_error,
+            logger.explore(
+                "Profile health preference additive migration failed",
+                extra={"src": "database", "error": str(migration_error)},
             )
 
 
@@ -244,9 +244,9 @@ def _ensure_llm_validation_results_columns(bind_engine):
                 for statement in alter_statements:
                     connection.execute(text(statement))
         except Exception as migration_error:
-            logger.warning(
-                "[database][EXPLORE] ValidationRecord additive migration failed: %s",
-                migration_error,
+            logger.explore(
+                "ValidationRecord additive migration failed",
+                extra={"src": "database", "error": str(migration_error)},
             )
 
 
@@ -284,9 +284,9 @@ def _ensure_git_server_configs_columns(bind_engine):
                 for statement in alter_statements:
                     connection.execute(text(statement))
         except Exception as migration_error:
-            logger.warning(
-                "[database][EXPLORE] GitServerConfig preference additive migration failed: %s",
-                migration_error,
+            logger.explore(
+                "GitServerConfig preference additive migration failed",
+                extra={"src": "database", "error": str(migration_error)},
             )
 
 
@@ -345,9 +345,9 @@ def _ensure_auth_users_columns(bind_engine):
                 },
             )
         except Exception as migration_error:
-            logger.warning(
-                "[database][EXPLORE] Auth users additive migration failed: %s",
-                migration_error,
+            logger.explore(
+                "Auth users additive migration failed",
+                extra={"src": "database", "error": str(migration_error)},
             )
             raise
 
@@ -365,9 +365,9 @@ def ensure_connection_configs_table(bind_engine):
         try:
             ConnectionConfig.__table__.create(bind=bind_engine, checkfirst=True)
         except Exception as migration_error:
-            logger.warning(
-                "[database][EXPLORE] ConnectionConfig table ensure failed: %s",
-                migration_error,
+            logger.explore(
+                "ConnectionConfig table ensure failed",
+                extra={"src": "database", "error": str(migration_error)},
             )
             raise
 
@@ -437,9 +437,9 @@ def _ensure_filter_source_enum_values(bind_engine):
                     extra={"added": missing_values},
                 )
         except Exception as migration_error:
-            logger.warning(
-                "[database][EXPLORE] FilterSource enum additive migration failed: %s",
-                migration_error,
+            logger.explore(
+                "FilterSource enum additive migration failed",
+                extra={"src": "database", "error": str(migration_error)},
             )