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/run.py

@@ -11,9 +11,8 @@
 import os
 import socket
 import httpx
-import logging
 
-logger = logging.getLogger("cot")
+from src.core.logger import logger
 
 FASTAPI_URL = os.getenv("FASTAPI_URL", "http://localhost:8000")
 
@@ -46,16 +45,37 @@ def _fetch_llm_config() -> dict | None:
             resp.raise_for_status()
             config = resp.json()
             if config.get("configured"):
-                logger.info("LLM config fetched from FastAPI: %s (%s)", config.get("provider_type"), config.get("default_model"))
+                logger.reason(
+                    "LLM config fetched from FastAPI",
+                    payload={"provider_type": config.get("provider_type"), "model": config.get("default_model")},
+                    extra={"src": "AgentChat.Run.FetchLlmConfig"},
+                )
                 return config
-            logger.warning("FastAPI returned no active LLM provider: %s", config.get("reason"))
+            logger.explore(
+                "FastAPI returned no active LLM provider",
+                payload={"reason": config.get("reason")},
+                error="No configured LLM provider",
+                extra={"src": "AgentChat.Run.FetchLlmConfig"},
+            )
         except Exception as e:
             if attempt < 5:
-                logger.info("Waiting for FastAPI (attempt %d/6): %s", attempt + 1, e)
+                logger.reason(
+                    f"Waiting for FastAPI (attempt {attempt + 1}/6)",
+                    payload={"error": str(e)},
+                    extra={"src": "AgentChat.Run.FetchLlmConfig"},
+                )
                 time.sleep(5)
             else:
-                logger.warning("Failed to fetch LLM config from FastAPI after 6 attempts: %s", e)
-                logger.info("Falling back to env vars for LLM config")
+                logger.explore(
+                    "Failed to fetch LLM config after 6 attempts",
+                    error=str(e),
+                    extra={"src": "AgentChat.Run.FetchLlmConfig"},
+                )
+                logger.explore(
+                    "Falling back to env vars for LLM config",
+                    error="FastAPI unreachable",
+                    extra={"src": "AgentChat.Run.FetchLlmConfig"},
+                )
     return None
 
 
@@ -85,9 +105,18 @@ if __name__ == "__main__":
         try:
             port = _find_free_port(configured_port)
             if port != configured_port:
-                logger.warning("Port %d is in use, falling back to port %d", configured_port, port)
+                logger.explore(
+                    "Port in use, falling back",
+                    payload={"configured_port": configured_port, "actual_port": port},
+                    error=f"Port {configured_port} is in use",
+                    extra={"src": "AgentChat.Run.PortBinding"},
+                )
         except OSError as e:
-            logger.error("Failed to find a free port: %s", e)
+            logger.explore(
+                "Failed to find a free port",
+                error=str(e),
+                extra={"src": "AgentChat.Run.PortBinding"},
+            )
             raise
     else:
         port = configured_port