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feat: Migrate MessageHub from command/query to unified request/onRequest API

This commit migrates the entire codebase from the old command/query API
to a unified request/onRequest API, simplifying RPC communication.

## Key Changes:

### Shared Layer (packages/shared)
- **types.ts**: Add RequestHandler type, keep old types for backward compat
- **message-hub.ts**:
  - Add request() method replacing command/query
  - Add onRequest() method replacing onCommand/onQuery
  - Add requestHandlers Map for unified handler storage
  - Update handleIncomingQuery with auto-ACK support
  - Keep old methods temporarily for smoother migration
- **protocol.ts**: Simplify message types (remove CALL/RESULT/SUBSCRIBE)
- **router.ts**: Update routing logic for new protocol
- **typed-hub.ts**: Update typed wrapper for new API
- **transports**: Update in-process and websocket transports
- **Add room-manager.ts**: New room-based routing system

### Daemon Layer (packages/daemon)
- **rpc-handlers/**: Migrate all 85 handlers from onCommand/onQuery to onRequest
- **app.ts**: Update handler registration
- **state-manager.ts**: Use new request API
- **routes/setup-websocket.ts**: Update for new protocol
- **Remove subscription-manager.ts**: No longer needed with new API

### Web Layer (packages/web)
- **hooks/useMessageHub.ts**:
  - Add request() method
  - Add onEvent() method
  - Keep old call/subscribe as deprecated aliases
- **lib/connection-manager.ts**: Update to use request
- **lib/session-store.ts**: Update to use request
- **lib/api-helpers.ts**: Update to use request
- **lib/state-channel.ts**: Update to use request
- **lib/global-store.ts**: Update to use request
- **components**: Update all components to use request/onEvent

### Tests
- Update all tests across packages/daemon, packages/shared, packages/web
- Update test helpers to use new API
- Remove cache.test.ts and stdio-transport.test.ts (deprecated)

## Benefits:
1. Simpler mental model: one method for request... (continued)

3322 of 16099 relevant lines covered (20.63%)

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Source Files on job daemon-offline-mcp - 21810006476.5