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/fileHistory.ts

@@ -1109,7 +1109,6 @@ async function readFileAsyncOrNull(path: string): Promise<string | null> {
 const ENABLE_DUMP_STATE = false
 function maybeDumpStateForDebug(state: FileHistoryState): void {
   if (ENABLE_DUMP_STATE) {
-    // biome-ignore lint/suspicious/noConsole:: intentional console output
     console.error(inspect(state, false, 5))
   }
 }