Add Agent class architecture documentation

This documentation provides a deep dive into the layered architecture
of the Agent class (DurableObject → Server → Agent), explaining how
each layer builds upon the previous one and what features each provides.

This helps developers understand the internals of the Agent class and
avoid common pitfalls when building agents.

Synced from cloudflare/agents PR #636

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Co-Authored-By: Claude <[email protected]>

Author: claude