Document Registry integration differences between Manifold and Automata

[fogfish]

Problem: Registry is used differently in Manifold (automatic) vs Automata (manual), but this isn't documented.

Required Changes:

1. Add section to README.md comparing registry usage
2. Add code example showing Automata with registry
3. Update registry.go godoc with usage examples
4. Add comment in agent/manifold.go explaining automatic handling
5. Add comment in agent/automata.go explaining decoder responsibility

Content to Add (README.md):

### Registry Integration Patterns

The Registry interface is integrated differently depending on the agent type:

**Manifold** - Automatic tool handling:
```go
registry := command.NewRegistry()
registry.Attach("calc", calculatorServer)

agent := agent.NewManifold(llm, encoder, decoder, registry)
// Registry is automatically called when LLM requests tools

Automata - Manual decoder handling:

func (a *MyAgent) Decode(reply *chatter.Reply) (float64, Result, error) {
    // Decoder must check for tool invocations
    if reply.Stage == chatter.LLM_INVOKE {
        // Handle tool calls manually
        phase, msg, err := a.registry.Invoke(reply)
        // ... process results
    }
    // ... decode normal responses
}

See examples/03_context (Manifold) and create new example for Automata pattern.

Estimated Effort: 1.5 hours
Skills Required: Technical writing, understanding of both agent types