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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tests/package-files.test.ts

@@ -43,6 +43,19 @@ test("every declared extension entry and file: dependency manifest is inside the
 	}
 });
 
+test("every file: dependency ships an UPSTREAM.md source record", () => {
+	for (const [name, specifier] of Object.entries(packageJson.dependencies)) {
+		const match = /^file:\.\/(.+)$/u.exec(specifier);
+		if (!match) continue;
+		const upstream = `${match[1]}/UPSTREAM.md`;
+		assert.ok(
+			readFileSync(join(repositoryRoot, upstream), "utf8").trim().length > 0,
+			`${name} is a file: dependency — ${upstream} must exist and be non-empty`,
+		);
+		assert.ok(packedFiles.has(upstream), `${name} is a file: dependency — ${upstream} must be packed`);
+	}
+});
+
 test("relative import specifiers inside packed sources resolve to packed files", () => {
 	const specifierPatterns = [
 		/\bfrom\s+["'](\.{1,2}\/[^"']+)["']/gu,