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/app.py

@@ -27,6 +27,7 @@ from .dependencies import get_task_manager, get_scheduler_service
 from .core.encryption_key import ensure_encryption_key
 from .core.utils.network import NetworkError
 from .core.logger import logger, belief_scope
+from .core.cot_logger import seed_trace_id
 from .core.database import AuthSessionLocal
 from .core.auth.security import get_password_hash
 from .models.auth import User, Role
@@ -130,6 +131,7 @@ def ensure_initial_admin_user() -> None:
 # Startup event
 @app.on_event("startup")
 async def startup_event():
+    seed_trace_id()
     with belief_scope("startup_event"):
         ensure_encryption_key()
         ensure_initial_admin_user()
@@ -148,6 +150,7 @@ async def startup_event():
 # Shutdown event
 @app.on_event("shutdown")
 async def shutdown_event():
+    seed_trace_id()
     with belief_scope("shutdown_event"):
         scheduler = get_scheduler_service()
         scheduler.stop()
@@ -170,6 +173,7 @@ app.add_middleware(
     allow_methods=["*"],
     allow_headers=["*"],
 )
+
 # #endregion app_middleware
 
 
@@ -221,6 +225,12 @@ async def log_requests(request: Request, call_next):
 
 # #endregion log_requests
 
+# Seed trace_id on every request — MUST be the outermost middleware so trace_id
+# is seeded before log_requests (or any other middleware) runs.
+from .core.middleware.trace import TraceContextMiddleware
+
+app.add_middleware(TraceContextMiddleware)
+
 # #region API_Routes [C:3] [TYPE Block]
 # @BRIEF Register all FastAPI route groups exposed by the application entrypoint.
 # @RELATION DEPENDS_ON -> [FastAPI_App]