fix(agent): unify logging API + add molecular-cot coverage to agent module

Phase 1 — API unification:
- Replace direct log() from cot_logger with canonical logger.reason/reflect/explore
  across _confirmation.py, _persistence.py, _tool_resolver.py, app.py

Phase 2 — Gap filling:
- tools.py: add REASON/REFLECT/EXPLORE to 17 C3 tool functions (was 0 logs)
- app.py agent_handler (C4): add lifecycle REASON on entry, REFLECT on exit,
  EXPLORE on OutputParserException + general exception
- langgraph_setup.py create_agent (C4): add REASON with model/config_source,
  EXPLORE on env-var/InMemorySaver fallback, REFLECT on graph compilation
- _tool_resolver.py infer_tool_from_text (C3, 13 branches): REASON on inference
- _persistence.py: REFLECT on save_conversation success, EXPLORE on prefetch

Phase 3 — Plain log migration:
- middleware.py: plain logger.info() -> logger.reason()
- run.py: 7 plain logger.info/warning/error -> molecular REASON/EXPLORE

Phase 4 — Cleanup:
- cot_logger.py: deprecate MarkerLogger (@DEPRECATED + @REPLACED_BY)
- molecular-cot-logging SKILL.md: remove cot_span Section IV (never implemented),
  renumber sections V-VII -> IV-VI, add cot_span rejection rationale

Verification: pytest 27/27, axiom rebuild 5844/2993/0 warnings

backend/src/agent/middleware.py

@@ -7,11 +7,9 @@
 # @REJECTED ConfirmationRiskMiddleware rejected — LangGraph interrupt_before=DANGEROUS_TOOLS handles HITL natively.
 
 from datetime import UTC, datetime
-import logging
 
 from src.agent.context import get_user_jwt
-
-logger = logging.getLogger("cot")
+from src.core.logger import logger
 
 
 # #region AgentChat.Middleware.LoggingMiddleware [C:3] [TYPE Function] [SEMANTICS audit,tool,logging]
@@ -48,9 +46,10 @@ async def log_tool_event(event: dict, conversation_id: str) -> None:
         elif kind == "on_tool_error":
             audit_payload["error"] = str(data.get("error", ""))[:500]
 
-    logger.info(
-        "Tool audit: %(event_type)s — %(tool)s — conv=%(conversation_id)s",
-        audit_payload,
+    logger.reason(
+        "Tool audit event",
+        payload=audit_payload,
+        extra={"src": "AgentChat.Middleware.LoggingMiddleware"},
     )
 
     # TODO: Async write to assistant_audit table via REST call to FastAPI