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

Generated with [Devin](https://devin.ai)

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>

pi-tool-search/test/bundle-groups.test.ts

@@ -10,6 +10,7 @@ function tool(name: string): ToolInfo {
     name,
     description: `Full description for ${name}`,
     parameters: { type: "object", properties: {} } as ToolInfo["parameters"],
+    exposure: "direct",
     sourceInfo: { source: "extension", scope: "user", path: `/test/${name}.ts` } as unknown as ToolInfo["sourceInfo"],
   };
 }

pi-tool-search/test/catalog.test.ts

@@ -21,6 +21,7 @@ function tool(name: string, description: string): ToolInfo {
     name,
     description,
     parameters: { type: "object", properties: { query: { type: "string" } } } as ToolInfo["parameters"],
+    exposure: "direct",
     sourceInfo: { source: "extension", scope: "user", path: `/test/${name}.ts` } as unknown as ToolInfo["sourceInfo"],
   };
 }

pi-tool-search/test/config.test.ts

@@ -41,6 +41,7 @@ test("bundle defaults keep the committed tool list", () => {
     "skill_manage",
     "context_tree_query",
     "overflow_query",
+    "codemode",
   ]);
   assert.deepEqual(bundleFallbackConfig(), {
     alwaysEnabled: [...BUNDLE_TOOL_SEARCH_DEFAULTS.alwaysEnabled],

pi-tool-search/test/extension.test.ts

@@ -5,7 +5,7 @@ import { join } from "node:path";
 import test from "node:test";
 
 import type { ExtensionAPI, ExtensionContext } from "@earendil-works/pi-coding-agent";
-import toolSearchExtension, { platformToolPolicy } from "../extensions/index.ts";
+import toolSearchExtension, { createToolSearchExtension, platformToolPolicy } from "../extensions/index.ts";
 
 interface ToolSearchResult {
   details: {
@@ -49,13 +49,12 @@ function testContext(overrides: Partial<ExtensionContext> = {}): ExtensionContex
 test("loads whole groups and evicts the least-recently-used group", async () => {
   const agentDir = await mkdtemp(join(tmpdir(), "my-pi-tool-search-extension-"));
   const previousAgentDir = process.env.PI_CODING_AGENT_DIR;
-  const previousConfigPath = process.env.PI_TOOL_SEARCH_CONFIG_PATH;
+  const configPath = join(agentDir, "tool-search-config.json");
   process.env.PI_CODING_AGENT_DIR = agentDir;
-  process.env.PI_TOOL_SEARCH_CONFIG_PATH = join(agentDir, "tool-search-config.json");
 
   try {
     await writeFile(
-      process.env.PI_TOOL_SEARCH_CONFIG_PATH,
+      configPath,
       JSON.stringify({
         alwaysEnabled: ["codegraph_explore", "lsp_diagnostics"],
         showToolSearchFooterStatus: false,
@@ -97,7 +96,7 @@ test("loads whole groups and evicts the least-recently-used group", async () =>
       on: (event: string, handler: (...args: any[]) => unknown) => handlers.set(event, handler),
     } as unknown as ExtensionAPI;
 
-    toolSearchExtension(api);
+    createToolSearchExtension({ configPath })(api);
     const ctx = testContext({
       hasUI: true,
       ui: {
@@ -159,8 +158,6 @@ test("loads whole groups and evicts the least-recently-used group", async () =>
   } finally {
     if (previousAgentDir === undefined) delete process.env.PI_CODING_AGENT_DIR;
     else process.env.PI_CODING_AGENT_DIR = previousAgentDir;
-    if (previousConfigPath === undefined) delete process.env.PI_TOOL_SEARCH_CONFIG_PATH;
-    else process.env.PI_TOOL_SEARCH_CONFIG_PATH = previousConfigPath;
     await rm(agentDir, { recursive: true, force: true });
   }
 });
@@ -328,6 +325,57 @@ test("keeps PowerShell with Bash only on Windows", () => {
   assert.ok(windows.coreTools.includes("powershell"));
 });
 
+test("drops hidden and script-only tools but keeps reachable exposures", () => {
+  const definitions = [
+    sourceTool("read", "Read a file"),
+    { ...sourceTool("hidden_helper", "Internal helper"), exposure: "hidden" },
+    { ...sourceTool("script_only", "Only callable from scripts"), exposure: "codemode" },
+    { ...sourceTool("codemode", "Batch several tool calls in one script"), exposure: "model-only" },
+    { ...sourceTool("lazy_tool", "Activated on demand"), exposure: "deferred" },
+  ];
+
+  const { tools } = platformToolPolicy(definitions, "darwin");
+  assert.deepEqual(tools.map((tool) => tool.name), ["read", "codemode", "lazy_tool"]);
+});
+
+test("pins a model-only codemode tool instead of hiding it", async () => {
+  const agentDir = await mkdtemp(join(tmpdir(), "my-pi-tool-search-codemode-"));
+  const previousAgentDir = process.env.PI_CODING_AGENT_DIR;
+  process.env.PI_CODING_AGENT_DIR = agentDir;
+
+  try {
+    const handlers = new Map<string, (...args: any[]) => unknown>();
+    const registered = new Map<string, RegisteredTool>();
+    const activeCalls: string[][] = [];
+    const sourceTools = [
+      sourceTool("read", "Read a file"),
+      { ...sourceTool("codemode", "Batch several tool calls in one script"), exposure: "model-only" },
+    ];
+    const api = {
+      getAllTools: () => sourceTools,
+      registerTool: (definition: unknown) => {
+        const tool = definition as RegisteredTool & { name: string };
+        registered.set(tool.name, tool);
+      },
+      registerCommand: () => {},
+      setActiveTools: (names: string[]) => activeCalls.push([...names]),
+      on: (event: string, handler: (...args: any[]) => unknown) => handlers.set(event, handler),
+    } as unknown as ExtensionAPI;
+    // The bundle config pins "codemode" in alwaysEnabled; exposure "model-only"
+    // stays reachable, so it must land in the active set, not a dynamic group.
+    toolSearchExtension(api);
+    handlers.get("session_start")?.({}, testContext());
+
+    assert.ok(activeCalls.at(-1)?.includes("codemode"));
+    assert.ok(activeCalls.at(-1)?.includes("tool_search"));
+    assert.ok(activeCalls.at(-1)?.includes("read"));
+  } finally {
+    if (previousAgentDir === undefined) delete process.env.PI_CODING_AGENT_DIR;
+    else process.env.PI_CODING_AGENT_DIR = previousAgentDir;
+    await rm(agentDir, { recursive: true, force: true });
+  }
+});
+
 test("loads an exact known group without waiting for unknown-tool model enrichment", async () => {
   const agentDir = await mkdtemp(join(tmpdir(), "my-pi-tool-search-fast-path-"));
   const previousAgentDir = process.env.PI_CODING_AGENT_DIR;