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/shell/prefix.ts

@@ -203,7 +203,6 @@ async function getCommandPrefixImpl(
         if (nonInteractive) {
           process.stderr.write(jsonStringify({ level: 'warn', message }) + '\n')
         } else {
-          // biome-ignore lint/suspicious/noConsole: intentional warning
           console.warn(chalk.yellow(`⚠️  ${message}`))
         }
       },