Add configuration, graph, runner, and tools modules to enhance agent functionality. Introduce a Configuration class for managing parameters, implement an AgentRunner for executing the agent graph, and create tools for general search and mathematical calculations. Update test_agent.py to reflect new import paths and improve overall code organization.

Refactor app.py and update import paths in test_agent.py to improve code organization. Introduce new files for agent configuration, graph definition, and tools, enhancing the overall structure and functionality of the agent system.

Refactor agent.py and graph.py to enhance agent functionality and logging. Introduce Configuration class for managing parameters, improve state handling in AgentRunner, and update agent graph to support step logging and user interaction. Add new tests for agent capabilities and update requirements for code formatting tools.