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
busya
a0619ca049