refactor(cli): split command routing and modularize RPC handlers

Restructure CLI entry point and RPC handler registration to improve maintainability:

- Introduce command registry pattern with CommandDefinition interface for consistent command structure
- Extract individual command modules (claude, codex, daemon, doctor, gemini, auth, connect, etc.)
- Move RPC handlers into separate feature modules (bash, files, git, directories, ripgrep, difftastic, slashCommands)
- Create shared RPC types and response helpers (rpcTypes.ts, rpcResponses.ts)
- Move SpawnSessionOptions and SpawnSessionResult to rpcTypes for proper type organization
- Simplify index.ts to minimal entrypoint using command registry
- Update imports in apiMachine.ts and daemon/run.ts to use rpcTypes module

This enables:
- Better code organization by feature/command
- Easier testing of individual commands
- Safer RPC handler registration without side effects
- Clearer separation of concerns between routing and business logic

cli/src/api/apiMachine.ts

@@ -10,7 +10,8 @@ import type { DaemonState, Machine, MachineMetadata, Update, UpdateMachineBody }
 import { DaemonStateSchema, MachineMetadataSchema } from './types'
 import { backoff } from '@/utils/time'
 import { RpcHandlerManager } from './rpc/RpcHandlerManager'
-import { registerCommonHandlers, type SpawnSessionOptions, type SpawnSessionResult } from '../modules/common/registerCommonHandlers'
+import { registerCommonHandlers } from '../modules/common/registerCommonHandlers'
+import type { SpawnSessionOptions, SpawnSessionResult } from '../modules/common/rpcTypes'
 
 interface ServerToDaemonEvents {
     update: (data: Update) => void