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

.opencode/skills/molecular-cot-logging/SKILL.md

@@ -9,7 +9,7 @@ description: Structured logging protocol for agent-driven development, based on
 @RELATION DISPATCHES -> [Std.Semantics.Python]
 @RELATION DISPATCHES -> [Std.Semantics.Svelte]
 @RATIONALE Long CoT chains need stabilisation through explicit reasoning bonds. The three-marker system (REASON/REFLECT/EXPLORE) maps directly to the molecular CoT paper and produces machine-readable execution traces that LLM agents can parse, analyse, and use for fine-tuning (MoLE-Syn bond distributions). Without structured markers, agent-generated code exhibits invisible failures: a function returns `None` instead of raising — the agent's attention never sees it because there's no log; a fallback path activates silently — no EXPLORE marker, no trace. JSON-line format ensures every log entry is a self-contained, parseable unit that survives log rotation, aggregation, and agent parsing — unlike plain-text logs that require regex heuristics.
-@REJECTED Legacy Entry/Exit/Action/Coherence markers rejected — they are too generic, do not map to reasoning structure, and prevent traceability graph analysis. Plain-text logging rejected — JSON lines are mandatory for agent parsing. Unstructured printf-style logging rejected — agents cannot reliably extract structured fields (trace_id, marker, intent) from free-form text, making automated diagnosis impossible.
+@REJECTED Legacy Entry/Exit/Action/Coherence markers rejected — they are too generic, do not map to reasoning structure, and prevent traceability graph analysis. Plain-text logging rejected — JSON lines are mandatory for agent parsing. Unstructured printf-style logging rejected — agents cannot reliably extract structured fields (trace_id, marker, intent) from free-form text, making automated diagnosis impossible. cot_span decorator rejected — replaced by belief_scope context manager + logger.reason/reflect/explore which gives more granular intent control per logical branch.
 @DATA_CONTRACT LogEntry -> { ts: str, level: str, trace_id: str, span_id?: str, src: str, marker: REASON|REFLECT|EXPLORE, intent: str, payload?: object, error?: str }
 @INVARIANT Every log line MUST carry exactly one valid marker (REASON | REFLECT | EXPLORE). No markerless log lines in C4/C5 code.
 @INVARIANT trace_id MUST propagate via ContextVar across async boundaries. Every incoming request or background job seeds a new trace_id.
@@ -207,58 +207,7 @@ class TraceMiddleware(BaseHTTPMiddleware):
         return response
 ```
 
-## IV. Python Decorator (Span + Marker)
-
-For C4/C5 functions, a decorator that auto-emits REASON / REFLECT markers:
-
-```python
-import asyncio
-from functools import wraps
-
-def cot_span(marker: str = "REASON", intent: str | None = None):
-    """Wrap a function in a CoT span.  On enter → REASON, on success → REFLECT,
-    on exception → EXPLORE."""
-    def decorator(func):
-        @wraps(func)
-        async def async_wrapper(*args, **kwargs):
-            src = f"{func.__module__}.{func.__qualname__}"
-            prev_span = push_span(func.__qualname__)
-            default_intent = intent or f"Execute {func.__qualname__}"
-            try:
-                log(src, marker, default_intent, payload=_summarise_args(args, kwargs))
-                result = await func(*args, **kwargs)
-                log(src, "REFLECT", f"{func.__qualname__} completed",
-                    payload={"result": _summarise_value(result)})
-                return result
-            except Exception as e:
-                log(src, "EXPLORE", f"{func.__qualname__} failed",
-                    error=str(e), payload={"args": _summarise_args(args, kwargs)})
-                raise
-            finally:
-                pop_span(prev_span)
-
-        @wraps(func)
-        def sync_wrapper(*args, **kwargs):
-            ...  # same logic, sync variant
-        return async_wrapper if asyncio.iscoroutinefunction(func) else sync_wrapper
-    return decorator
-
-
-def _summarise_value(val, max_len: int = 200) -> str:
-    s = str(val)
-    return s[:max_len] + "..." if len(s) > max_len else s
-
-def _summarise_args(args, kwargs) -> dict:
-    # Skip 'self', 'cls', 'db', 'request' — too verbose
-    skip = {"self", "cls", "db", "request", "session"}
-    result = {}
-    for k, v in kwargs.items():
-        if k not in skip:
-            result[k] = _summarise_value(v)
-    return result
-```
-
-## V. Svelte / Frontend Pattern
+## IV. Svelte / Frontend Pattern
 
 The frontend implementation lives at `frontend/src/lib/cot-logger.ts` (installed as `$lib/cot-logger`).
 
@@ -321,7 +270,7 @@ const res = await requestApi("/api/endpoint");
 if (res.trace_id) setTraceId(res.trace_id);
 ```
 
-## VI. CLI / Stdout Reader (for humans)
+## V. CLI / Stdout Reader (for humans)
 
 To make JSON lines readable in development:
 
@@ -341,7 +290,7 @@ for line in sys.stdin:
 "
 ```
 
-## VII. Anti-patterns
+## VI. Anti-patterns
 
 | ❌ Don't | ✅ Do |
 |----------|-------|