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/test/config.test.ts

@@ -1,10 +1,16 @@
 import assert from "node:assert/strict";
-import { mkdtemp, readFile, rm, stat, writeFile } from "node:fs/promises";
+import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
-import { join } from "node:path";
+import { dirname, join } from "node:path";
 import test from "node:test";
 
-import { BUNDLE_TOOL_SEARCH_DEFAULTS, ensureToolSearchDefaults, readToolSearchConfig } from "../extensions/config.ts";
+import {
+  BUNDLE_TOOL_SEARCH_DEFAULTS,
+  bundleFallbackConfig,
+  getToolSearchCatalogPath,
+  getToolSearchConfigPath,
+  readToolSearchConfig,
+} from "../extensions/config.ts";
 
 async function withAgentDir(run: (agentDir: string) => Promise<void>): Promise<void> {
   const agentDir = await mkdtemp(join(tmpdir(), "my-pi-tool-search-"));
@@ -15,71 +21,73 @@ async function withAgentDir(run: (agentDir: string) => Promise<void>): Promise<v
   }
 }
 
-test("writes bundle defaults when toolSearch is absent", async () => {
-  await withAgentDir(async (agentDir) => {
-    assert.equal(ensureToolSearchDefaults(agentDir), "updated");
-    assert.deepEqual(BUNDLE_TOOL_SEARCH_DEFAULTS.alwaysEnabled, [
-      "codegraph_explore",
-      "lsp_diagnostics",
-      "ctx_execute",
-      "ctx_execute_file",
-      "ctx_batch_execute",
-      "memory_search",
-      "session_search",
-      "memory_add",
-      "memory_replace",
-      "memory_remove",
-      "skill_manage",
-      "context_tree_query",
-    ]);
-    assert.deepEqual(JSON.parse(await readFile(join(agentDir, "settings.json"), "utf8")), {
-      toolSearch: {
-        alwaysEnabled: [...BUNDLE_TOOL_SEARCH_DEFAULTS.alwaysEnabled],
-        showToolSearchFooterStatus: false,
-        maxActiveGroups: 5,
-        maxToolsPerGroup: 8,
-        maxDynamicTools: 28,
-        groupOverrides: {},
-        bundleDefaultsVersion: 4,
-      },
-    });
-    assert.equal((await stat(join(agentDir, "settings.json"))).mode & 0o777, 0o600);
+async function writeConfig(agentDir: string, content: string): Promise<void> {
+  const path = getToolSearchConfigPath(agentDir);
+  await mkdir(dirname(path), { recursive: true });
+  await writeFile(path, content, "utf8");
+}
+
+test("bundle defaults keep the committed tool list", () => {
+  assert.deepEqual(BUNDLE_TOOL_SEARCH_DEFAULTS.alwaysEnabled, [
+    "codegraph_explore",
+    "lsp_diagnostics",
+    "ctx_execute",
+    "ctx_execute_file",
+    "ctx_batch_execute",
+    "memory_search",
+    "session_search",
+    "memory_add",
+    "memory_replace",
+    "memory_remove",
+    "skill_manage",
+    "context_tree_query",
+  ]);
+  assert.deepEqual(bundleFallbackConfig(), {
+    alwaysEnabled: [...BUNDLE_TOOL_SEARCH_DEFAULTS.alwaysEnabled],
+    showToolSearchFooterStatus: false,
+    maxActiveGroups: 5,
+    maxToolsPerGroup: 8,
+    maxDynamicTools: 28,
+    groupOverrides: {},
   });
 });
 
-test("fills missing defaults and preserves explicit settings", async () => {
+test("config and catalog live under the bundle-owned my-pi tree", async () => {
   await withAgentDir(async (agentDir) => {
-    const path = join(agentDir, "settings.json");
-    await writeFile(path, JSON.stringify({ theme: "dark", toolSearch: { alwaysEnabled: ["multi_grep"], maxActiveGroups: 2 } }), "utf8");
-    assert.equal(ensureToolSearchDefaults(agentDir), "updated");
-    assert.deepEqual(JSON.parse(await readFile(path, "utf8")), {
-      theme: "dark",
-      toolSearch: {
-        alwaysEnabled: ["multi_grep"],
-        maxActiveGroups: 2,
-        showToolSearchFooterStatus: false,
-        maxToolsPerGroup: 8,
-        maxDynamicTools: 28,
-        groupOverrides: {},
-      },
-    });
+    assert.equal(
+      getToolSearchConfigPath(agentDir),
+      join(agentDir, "my-pi", "tool-search", "config.json"),
+    );
+    assert.equal(
+      getToolSearchCatalogPath(agentDir),
+      join(agentDir, "my-pi", "tool-search", "catalog-v1.json"),
+    );
+  });
+});
+
+test("falls back to bundle defaults when the config file is absent or invalid", async () => {
+  await withAgentDir(async (agentDir) => {
+    assert.deepEqual(readToolSearchConfig(agentDir), bundleFallbackConfig());
+
+    await writeConfig(agentDir, "{not-json");
+    assert.deepEqual(readToolSearchConfig(agentDir), bundleFallbackConfig());
+
+    await writeConfig(agentDir, '"a string, not an object"');
+    assert.deepEqual(readToolSearchConfig(agentDir), bundleFallbackConfig());
   });
 });
 
 test("normalizes invalid runtime values without overwriting the file", async () => {
   await withAgentDir(async (agentDir) => {
-    const path = join(agentDir, "settings.json");
     const original = JSON.stringify({
-      toolSearch: {
-        alwaysEnabled: ["one", "one", 3],
-        showToolSearchFooterStatus: "no",
-        maxActiveGroups: 0,
-        maxToolsPerGroup: 4,
-        maxDynamicTools: -1,
-        groupOverrides: { web: ["search", 2], empty: [] },
-      },
+      alwaysEnabled: ["one", "one", 3],
+      showToolSearchFooterStatus: "no",
+      maxActiveGroups: 0,
+      maxToolsPerGroup: 4,
+      maxDynamicTools: -1,
+      groupOverrides: { web: ["search", 2], empty: [] },
     });
-    await writeFile(path, original, "utf8");
+    await writeConfig(agentDir, original);
     assert.deepEqual(readToolSearchConfig(agentDir), {
       alwaysEnabled: ["one"],
       showToolSearchFooterStatus: false,
@@ -88,34 +96,29 @@ test("normalizes invalid runtime values without overwriting the file", async ()
       maxDynamicTools: 28,
       groupOverrides: { web: ["search"] },
     });
-    assert.equal(await readFile(path, "utf8"), original);
+    assert.equal(await readFile(getToolSearchConfigPath(agentDir), "utf8"), original);
   });
 });
 
-test("preserves a complete explicit configuration including former defaults", async () => {
+test("reads an explicit configuration verbatim", async () => {
   await withAgentDir(async (agentDir) => {
-    const path = join(agentDir, "settings.json");
     const original = `${JSON.stringify({
-      toolSearch: {
-        alwaysEnabled: ["codegraph_explore", "lsp_diagnostics"],
-        showToolSearchFooterStatus: false,
-        maxActiveGroups: 3,
-        maxToolsPerGroup: 8,
-        maxDynamicTools: 20,
-        groupOverrides: {},
-      },
+      alwaysEnabled: ["codegraph_explore", "lsp_diagnostics"],
+      showToolSearchFooterStatus: true,
+      maxActiveGroups: 3,
+      maxToolsPerGroup: 8,
+      maxDynamicTools: 20,
+      groupOverrides: { custom: ["some_tool"] },
     }, null, 2)}\n`;
-    await writeFile(path, original, "utf8");
-    assert.equal(ensureToolSearchDefaults(agentDir), "unchanged");
-    assert.equal(await readFile(path, "utf8"), original);
-  });
-});
-
-test("does not overwrite malformed settings", async () => {
-  await withAgentDir(async (agentDir) => {
-    const path = join(agentDir, "settings.json");
-    await writeFile(path, "{not-json", "utf8");
-    assert.equal(ensureToolSearchDefaults(agentDir), "skipped-invalid");
-    assert.equal(await readFile(path, "utf8"), "{not-json");
+    await writeConfig(agentDir, original);
+    assert.deepEqual(readToolSearchConfig(agentDir), {
+      alwaysEnabled: ["codegraph_explore", "lsp_diagnostics"],
+      showToolSearchFooterStatus: true,
+      maxActiveGroups: 3,
+      maxToolsPerGroup: 8,
+      maxDynamicTools: 20,
+      groupOverrides: { custom: ["some_tool"] },
+    });
+    assert.equal(await readFile(getToolSearchConfigPath(agentDir), "utf8"), original);
   });
 });