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/tests/test_smoke_app.py

@@ -0,0 +1,83 @@
+# [DEF:TestSmokeApp:Module]
+# @COMPLEXITY: 2
+# @SEMANTICS: tests, smoke, app, imports, fastapi
+# @PURPOSE: Minimal smoke tests that verify the full application import chain
+#           succeeds without SyntaxError, IndentationError, ImportError, or
+#           NameError in any module.
+# @LAYER: Tests (Smoke)
+# @RELATION: VERIFIES -> src/app.py
+# @RELATION: VERIFIES -> src/core/cot_logger.py
+# @INVARIANT: All tests must pass without a running PostgreSQL instance.
+#
+# @RATIONALE: Uses SQLite in-memory database URLs to avoid requiring a live
+#             PostgreSQL server during smoke testing. The database module's
+#             _build_engine() already supports SQLite with
+#             check_same_thread=False.
+
+"""Smoke test: verify the full application imports without errors.
+
+Catches: SyntaxError, IndentationError, ImportError, NameError in any module
+that is part of the application import chain.
+
+Database dependency:
+    The application's database module (src.core.database) creates SQLAlchemy
+    engines at import time. To avoid needing a running PostgreSQL instance,
+    environment variables are set to SQLite in-memory databases before the
+    app is imported.
+"""
+
+import os
+import sys
+from pathlib import Path
+
+# ---------------------------------------------------------------------------
+# Database URL override: use SQLite in-memory so no PostgreSQL is needed.
+# Must happen before ANY application module is imported.
+# ---------------------------------------------------------------------------
+os.environ.setdefault("DATABASE_URL", "sqlite:///:memory:")
+os.environ.setdefault("TASKS_DATABASE_URL", "sqlite:///:memory:")
+os.environ.setdefault("AUTH_DATABASE_URL", "sqlite:///:memory:")
+
+# Ensure the backend root is on sys.path so `src` package is importable
+_src_path = str(Path(__file__).resolve().parent.parent)
+if _src_path not in sys.path:
+    sys.path.insert(0, _src_path)
+
+
+def test_app_imports_cleanly():
+    """The application module tree imports without errors."""
+    from src.app import app
+
+    assert app is not None
+    assert app.title == "Superset Tools API"
+
+
+def test_app_has_expected_middleware():
+    """TraceContextMiddleware is registered (trace_id propagation)."""
+    from src.app import app
+
+    middleware_classes = [m.cls.__name__ for m in app.user_middleware]
+    assert "TraceContextMiddleware" in middleware_classes, (
+        f"TraceContextMiddleware not found in app middleware: {middleware_classes}"
+    )
+
+
+def test_cot_logger_imports():
+    """Core logging infrastructure is importable."""
+    from src.core.cot_logger import (
+        log,
+        seed_trace_id,
+        get_trace_id,
+        push_span,
+        pop_span,
+    )
+
+    tid = seed_trace_id()
+    assert tid is not None
+    assert get_trace_id() == tid
+    log("test", "REASON", "Smoke test log entry", {"ok": True})
+
+    # Verify push_span / pop_span round-trip
+    prev = push_span("test_span")
+    assert prev == ""  # default empty span
+    pop_span(prev)