feat: 接入 Pi 内置 codemode，并修复全面审查发现的问题

- codemode：Tool Search 常驻（alwaysEnabled）、权限 allow（嵌套调用仍逐个过权限门）、
  tools.jsonc 登记使用规则；RTK 跳过 parentToolCallId 嵌套调用，避免丢失 bash
  structuredContent；Tool Search 目录过滤 hidden / codemode（script-only）exposure；
  扩展加载测试加载 builtin:codemode 并断言其常驻激活
- 搜索 key 不再经命令行参数传递：search-auth.mjs 改为 --set-stdin（先读校验再加锁），
  configure.sh 交互输入经管道、非交互用 --<provider> -
- CodeGraph 客户端监听子进程 stdin error，避免 EPIPE 未处理导致崩溃
- 移除 PI_TOOL_SEARCH/HERMES_MEMORY/RTK_CONFIG_PATH 环境变量入口，测试改用工厂 configPath 注入
- pi-subagents 固定 vitest / coverage-istanbul 4.1.10，修复 npm ls 版本冲突
- 补 pi-web-search / pi-worktree UPSTREAM.md 与 pi-minimal-footer AGENTS.md，
  files 白名单补齐并加测试；.codegraph/.gitignore 移出跟踪
- detect_kitty 优先识别官方安装目录

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package.json

@@ -94,11 +94,13 @@
     "pi-web-search/package.json",
     "pi-web-search/README.md",
     "pi-web-search/LICENSE",
+    "pi-web-search/UPSTREAM.md",
     "pi-worktree/index.ts",
     "pi-worktree/src",
     "pi-worktree/package.json",
     "pi-worktree/README.md",
     "pi-worktree/LICENSE",
+    "pi-worktree/UPSTREAM.md",
     "pi-permission-system/LICENSES",
     "pi-permission-system/docs/auto-review",
     "pi-permission-system/src",
@@ -107,6 +109,7 @@
     "pi-permission-system/README.md",
     "pi-permission-system/CHANGELOG.md",
     "pi-permission-system/LICENSE",
+    "pi-permission-system/UPSTREAM.md",
     "config",
     "scripts",
     "install.sh",