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>

tests/system-prompt-cover.test.ts

@@ -1,16 +1,10 @@
 import assert from "node:assert/strict";
-import { mkdtemp, readdir, readFile, rm, writeFile } from "node:fs/promises";
-import { execFileSync } from "node:child_process";
+import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { dirname, join, resolve } from "node:path";
 import test from "node:test";
 import { fileURLToPath } from "node:url";
 
-import {
-  COVER_FILE_NAME,
-  deploySystemPromptCover,
-  resolveAgentDir,
-} from "../scripts/deploy-system-prompt-cover.mjs";
 import {
   readCoverFile,
   resolveCoverPath,
@@ -149,8 +143,10 @@ test("readCoverFile returns undefined when the file is absent or blank", async (
   const dir = await makeTempDir();
   try {
     const coverPath = resolveCoverPath(dir);
+    assert.equal(coverPath, join(dir, "my-pi", "system-prompt-cover.md"));
     assert.equal(readCoverFile(coverPath), undefined);
 
+    await mkdir(dirname(coverPath), { recursive: true });
     await writeFile(coverPath, "   \n\n", "utf8");
     assert.equal(readCoverFile(coverPath), undefined);
 
@@ -160,58 +156,3 @@ test("readCoverFile returns undefined when the file is absent or blank", async (
     await rm(dir, { recursive: true, force: true });
   }
 });
-
-test("resolveAgentDir honours PI_CODING_AGENT_DIR and defaults to ~/.pi/agent", () => {
-  assert.equal(resolveAgentDir({}, "/home/u"), "/home/u/.pi/agent");
-  assert.equal(resolveAgentDir({ PI_CODING_AGENT_DIR: "/custom/agent" }, "/home/u"), "/custom/agent");
-  assert.equal(resolveAgentDir({ PI_CODING_AGENT_DIR: "~/other" }, "/home/u"), "/home/u/other");
-});
-
-test("deploySystemPromptCover creates, is idempotent, and overwrites without a backup", async () => {
-  const dir = await makeTempDir();
-  try {
-    const target = join(dir, COVER_FILE_NAME);
-
-    assert.equal((await deploySystemPromptCover({ agentDir: dir })).status, "created");
-    assert.equal(await readFile(target, "utf8"), await readFile(bundledCoverPath, "utf8"));
-
-    assert.equal((await deploySystemPromptCover({ agentDir: dir })).status, "current");
-
-    await writeFile(target, "USER EDITED COVER\n", "utf8");
-    assert.equal((await deploySystemPromptCover({ agentDir: dir })).status, "updated");
-    assert.equal(await readFile(target, "utf8"), await readFile(bundledCoverPath, "utf8"));
-
-    // No backup and no temporary file may survive an overwrite.
-    assert.deepEqual(await readdir(dir), [COVER_FILE_NAME]);
-  } finally {
-    await rm(dir, { recursive: true, force: true });
-  }
-});
-
-test("deploySystemPromptCover fails loudly when the bundled cover is unreadable", async () => {
-  const dir = await makeTempDir();
-  try {
-    await assert.rejects(
-      deploySystemPromptCover({ agentDir: dir, bundledCoverPath: join(dir, "missing.md") }),
-      /cannot read bundled system prompt cover/,
-    );
-    // The failure must not leave a partial file behind.
-    assert.deepEqual(await readdir(dir), []);
-  } finally {
-    await rm(dir, { recursive: true, force: true });
-  }
-});
-
-test("deploy-system-prompt-cover.mjs prints a status line and exits zero", async () => {
-  const dir = await makeTempDir();
-  try {
-    const helper = join(repositoryRoot, "scripts", "deploy-system-prompt-cover.mjs");
-    const first = execFileSync(process.execPath, [helper, dir], { encoding: "utf8" }).trim();
-    const second = execFileSync(process.execPath, [helper, dir], { encoding: "utf8" }).trim();
-
-    assert.equal(first, "created");
-    assert.equal(second, "current");
-  } finally {
-    await rm(dir, { recursive: true, force: true });
-  }
-});