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/core/cot_logger.py

@@ -170,6 +170,9 @@ def log(
 # #region MarkerLogger [C:2] [TYPE Class] [SEMANTICS logger, proxy, marker, syntactic-sugar]
 # @ingroup Core
 # @BRIEF Thin proxy class providing .reason(), .reflect(), .explore() convenience methods.
+# @DEPRECATED Use logger.reason/reflect/explore from src.core.logger instead — MarkerLogger has
+#             zero usages in the codebase and adds a redundant abstraction layer.
+# @REPLACED_BY logger.reason/reflect/explore (monkey-patched on superset_tools_app logger)
 class MarkerLogger:
     """Thin proxy over the cot_logger.log() function.