Refactor models and logging for nexus-claude-api

- Update default models in config to use `claude-opus-4.6`.
- Introduce logging configuration to write logs to a file.
- Add correlation ID to error responses for better traceability.
- Implement diagnostics for summarizing message requests.
- Normalize legacy system messages in the API.
- Enhance tests to cover new logging and error handling features.
- Update README and documentation to reflect changes in model defaults and logging behavior.

.gitignore

@@ -10,3 +10,11 @@ __pycache__/
 .env.*
 !.env.example
 nexus-claude-api.local.json
+
+# agents
+.omo
+.codegraph
+.agents
+
+# logs
+logs