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-permission-system/docs/configuration.md

@@ -6,8 +6,8 @@ Pi Permission System reads two user-level JSONC files:
 
 | Purpose | Scope | Path |
 | ------- | ----- | ---- |
-| Ordinary policy + runtime | Global only | `~/.pi/agent/extensions/pi-permission-system/policy.jsonc` |
-| Hard guards | Global only | `~/.pi/agent/extensions/pi-permission-system/hard-guards.jsonc` |
+| Ordinary policy + runtime | Global only | `~/.pi/agent/my-pi/permission-system/policy.jsonc` |
+| Hard guards | Global only | `~/.pi/agent/my-pi/permission-system/hard-guards.jsonc` |
 
 `PI_CODING_AGENT_DIR` replaces `~/.pi/agent` when set. Project-level `policy.jsonc` files are not loaded. Project agent Markdown may still provide per-agent restrictions; it is not a second ordinary policy file.
 
@@ -141,7 +141,7 @@ Each review outcome is written to the permission review log — the resolved mod
 | `toolTextSummaryMaxLength`  | —        | **Deprecated and ignored.** Superseded by `promptMaxRows` / `promptFieldMaxWidth`. Still accepted so an existing config is not rejected, but the value no longer applies; setting it logs a warning.                                         |
 | `authorizerChain`           | `[]`     | Ordered names of registered live-authority chain links to consult before the terminal authorizer (see [Authorizer chain](#authorizer-chain--case-by-case-decision-links)).                                                                   |
 
-Both logs write to `~/.pi/agent/extensions/pi-permission-system/logs/`.
+Both logs write to `~/.pi/agent/my-pi/permission-system/logs/`.
 No debug output is printed to the terminal.
 
 ### Inline permission dialog (TUI)