feat: 组合包配置集中到 my-pi/ 目录并改为整体重建

- 组合包拥有、可随时重建的配置、日志与缓存统一放在
  <agentDir>/my-pi/：permission-system/（policy.jsonc、hard-guards.jsonc、
  logs/）、rtk-optimizer/config.json、tool-search/（config.json、
  catalog-v1.json）与 system-prompt-cover.md。hashline.json、lsp.json
  由外部扩展读取固定路径，是唯一例外。
- 新增 config/bundle-manifest.json 与 scripts/rebuild-bundle-config.mjs：
  先校验全部来源与目标，在临时目录构建完整树，再整体删除旧 my-pi/
  （符号链接只删链接）并原子替换，不备份。install.sh / update.sh 每次
  运行都调用它；扩展自身不再播种或迁移配置。
- update.sh 删除 pi update 失败后的 git clean 恢复逻辑：Pi 1.3.0 会在
  下一次 pi update 时依据中断标记自行恢复。同时删除 Tool Search
  settings.json 快照迁移与封面部署脚本。
- Tool Search 改为读取 my-pi/tool-search/config.json（源为
  config/tool-search.json，须与 BUNDLE_TOOL_SEARCH_DEFAULTS 一致），
  不再读写 settings.json 的 toolSearch 段，移除 bundleDefaultsVersion。
- 默认权限策略开启 debugLog。
- 旧位置的残留文件不迁移、不清理；AGENTS.md / README 同步新约束。

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

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

pi-tool-search/extensions/config.ts

@@ -1,17 +1,21 @@
-import {
-  chmodSync,
-  closeSync,
-  fsyncSync,
-  mkdirSync,
-  openSync,
-  readFileSync,
-  renameSync,
-  rmSync,
-  writeFileSync,
-} from "node:fs";
-import { dirname, join } from "node:path";
+import { readFileSync } from "node:fs";
+import { join } from "node:path";
 
-export type ToolSearchDefaultResult = "updated" | "unchanged" | "skipped-invalid";
+const TOOL_SEARCH_DIR = join("my-pi", "tool-search");
+
+/**
+ * Path of the bundle-managed Tool Search config inside the agent directory.
+ * `scripts/rebuild-bundle-config.mjs` deploys `config/tool-search.json` here;
+ * this extension never writes or migrates it.
+ */
+export function getToolSearchConfigPath(agentDir: string): string {
+  return join(agentDir, TOOL_SEARCH_DIR, "config.json");
+}
+
+/** Catalog cache path under the same bundle-owned `my-pi/tool-search/` tree. */
+export function getToolSearchCatalogPath(agentDir: string): string {
+  return join(agentDir, TOOL_SEARCH_DIR, "catalog-v1.json");
+}
 
 export const BUNDLE_TOOL_SEARCH_DEFAULTS = {
   alwaysEnabled: [
@@ -35,8 +39,6 @@ export const BUNDLE_TOOL_SEARCH_DEFAULTS = {
   groupOverrides: {},
 } as const;
 
-export const BUNDLE_TOOL_SEARCH_DEFAULTS_VERSION = 4;
-
 export interface ToolSearchConfig {
   alwaysEnabled: string[];
   showToolSearchFooterStatus: boolean;
@@ -80,12 +82,16 @@ export function bundleFallbackConfig(): ToolSearchConfig {
   };
 }
 
+/**
+ * Read the Tool Search config from `<agentDir>/my-pi/tool-search/config.json`.
+ * A missing, unreadable, or non-object file falls back to the bundle defaults.
+ */
 export function readToolSearchConfig(agentDir: string): ToolSearchConfig {
   const fallback = bundleFallbackConfig();
   try {
-    const parsed: unknown = JSON.parse(readFileSync(join(agentDir, "settings.json"), "utf8"));
-    if (!isObject(parsed) || !isObject(parsed.toolSearch)) return fallback;
-    const config = parsed.toolSearch;
+    const parsed: unknown = JSON.parse(readFileSync(getToolSearchConfigPath(agentDir), "utf8"));
+    if (!isObject(parsed)) return fallback;
+    const config = parsed;
     return {
       alwaysEnabled: Array.isArray(config.alwaysEnabled) ? stringList(config.alwaysEnabled) : fallback.alwaysEnabled,
       showToolSearchFooterStatus:
@@ -101,52 +107,3 @@ export function readToolSearchConfig(agentDir: string): ToolSearchConfig {
     return fallback;
   }
 }
-
-/** Add bundle defaults without replacing explicit user choices. */
-export function ensureToolSearchDefaults(agentDir: string): ToolSearchDefaultResult {
-  const targetPath = join(agentDir, "settings.json");
-  let settings: Record<string, unknown> = {};
-
-  try {
-    const parsed: unknown = JSON.parse(readFileSync(targetPath, "utf8"));
-    if (!isObject(parsed)) return "skipped-invalid";
-    settings = parsed;
-  } catch (error) {
-    if ((error as NodeJS.ErrnoException).code !== "ENOENT") return "skipped-invalid";
-  }
-
-  const existing = settings.toolSearch;
-  if (existing !== undefined && !isObject(existing)) return "skipped-invalid";
-
-  const toolSearch = { ...(existing ?? {}) };
-  let changed = false;
-  for (const [key, value] of Object.entries(BUNDLE_TOOL_SEARCH_DEFAULTS)) {
-    if (Object.hasOwn(toolSearch, key)) continue;
-    toolSearch[key] = Array.isArray(value) ? [...value] : isObject(value) ? { ...value } : value;
-    changed = true;
-  }
-  if (existing === undefined) {
-    toolSearch.bundleDefaultsVersion = BUNDLE_TOOL_SEARCH_DEFAULTS_VERSION;
-    changed = true;
-  }
-  if (!changed) return "unchanged";
-
-  settings.toolSearch = toolSearch;
-  mkdirSync(dirname(targetPath), { recursive: true });
-  const temporaryPath = `${targetPath}.my-pi-${process.pid}-${Math.random().toString(16).slice(2)}.tmp`;
-  let descriptor: number | undefined;
-  try {
-    descriptor = openSync(temporaryPath, "wx", 0o600);
-    writeFileSync(descriptor, `${JSON.stringify(settings, null, 2)}\n`, "utf8");
-    fsyncSync(descriptor);
-    closeSync(descriptor);
-    descriptor = undefined;
-    renameSync(temporaryPath, targetPath);
-    chmodSync(targetPath, 0o600);
-  } catch (error) {
-    if (descriptor !== undefined) closeSync(descriptor);
-    rmSync(temporaryPath, { force: true });
-    throw error;
-  }
-  return "updated";
-}

pi-tool-search/extensions/index.ts

@@ -6,7 +6,6 @@
  */
 import { randomUUID } from "node:crypto";
 import { unlinkSync } from "node:fs";
-import { join } from "node:path";
 
 import { getAgentDir, type ExtensionAPI, type ExtensionContext, type ToolInfo } from "@earendil-works/pi-coding-agent";
 import { Type } from "typebox";
@@ -29,7 +28,7 @@ import {
   createBundleCatalog,
   type BundleCatalogResult,
 } from "./bundle-groups.ts";
-import { ensureToolSearchDefaults, readToolSearchConfig } from "./config.ts";
+import { getToolSearchCatalogPath, readToolSearchConfig } from "./config.ts";
 
 const TOOL_SEARCH_NAME = "tool_search";
 const POWERSHELL_TOOL_NAME = "powershell";
@@ -113,11 +112,7 @@ function groupDescription(catalog: ToolCatalog, source: CatalogSource): string {
 
 export default function toolSearchExtension(pi: ExtensionAPI): void {
   const agentDir = getAgentDir();
-  const cachePath = join(agentDir, "tool-search", "catalog-v1.json");
-  const defaultResult = ensureToolSearchDefaults(agentDir);
-  if (defaultResult === "skipped-invalid") {
-    console.warn("my-pi: skipped pi-tool-search defaults because settings.json or toolSearch is invalid");
-  }
+  const cachePath = getToolSearchCatalogPath(agentDir);
 
   let config = readToolSearchConfig(agentDir);
   let tools: ToolInfo[] = [];