Clarify recommended project structure and organization patterns for AgentKit-based apps

AgentKit is flexible and can be used in many different ways, but new users may struggle to understand how to structure a real-world project around it. The repository does not currently provide guidance on recommended file structure, separation of concerns, or scaling patterns for larger agent-based applications.

### Problem Description
Developers building with AgentKit may be unsure about:
- where to define agents vs tools vs providers
- how to organize long-running agents vs request-based agents
- how to separate configuration, execution logic, and orchestration
- how to scale from a simple demo to a production-ready setup

Without guidance, teams often invent their own structures, leading to inconsistent patterns and harder-to-maintain codebases.

### Expected Behavior
- Developers should have a reference for organizing AgentKit projects.
- Examples should demonstrate clean separation of concerns.
- Guidance should help teams avoid common structural pitfalls.

### Steps to Reproduce
1. Start a new project using AgentKit.
2. Add multiple agents, tools, and providers.
3. Attempt to organize the codebase in a scalable way.
4. Notice the lack of official guidance or examples.

### Proposed Solution
- Add a documentation section or guide such as “Project Structure & Architecture”.
- Provide one or two example directory layouts (small app vs larger app).
- Explain recommended separation between:
- agent definitions
- tools/providers
- configuration and runtime wiring
- Keep guidance opinionated but optional.