feat: 添加工具类增强与状态管理改进

- 新增 workflowRuns、remoteTriggerAudit、pipeStatus 等工具
- 增强 permissionSetup: auto mode 和 bypass permissions 始终可用
- 新增多组测试覆盖 (modifiers, teamDiscovery, deepLink 等)
- 修复 parseInt 缺少 radix 参数
- 移除多余 biome-ignore 注释

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/utils/slowOperations.ts

@@ -6,7 +6,6 @@ import {
   fsyncSync,
   openSync,
 } from 'fs'
-// biome-ignore lint: This file IS the cloneDeep wrapper - it must import the original
 import lodashCloneDeep from 'lodash-es/cloneDeep.js'
 import { addSlowOperation } from '../bootstrap/state.js'
 import { logForDebugging } from './debug.js'
@@ -132,6 +131,7 @@ function slowLoggingAnt(
   ..._values: unknown[]
 ): AntSlowLogger {
   // eslint-disable-next-line prefer-rest-params
+  // biome-ignore lint/complexity/noArguments: intentional use of arguments object for AntSlowLogger
   return new AntSlowLogger(arguments)
 }