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。

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pi-permission-system/CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Cache approvals within one user message.** An `allow` is reused for the same action while the conversation's latest trusted entry is unchanged; a new user message invalidates the cache, and rejects and failures are never cached.
 - Bound the rendered transcript with a conservative token estimator (ASCII counts a quarter token per character, every non-ASCII codepoint a full token — `length / 4` under-counts CJK by roughly 2–4x), expose the budgets under `autoReview.transcript` (`messageTokens`, `toolTokens`, `maxUntrustedEntries`), and substitute pi-compaction tool-result summaries when they are strictly shorter.
 - Make `autoReview.reasoning` effective again (default `"low"`), passed only to reasoning-capable models; add `autoReview.timeoutMs` (default `30000`, total across attempts), `autoReview.maxAttempts` (default `2`), and `autoReview.maxOutputTokens` (default `4000`).
+- **Move the global config directory into the bundle-owned rebuild tree.** Policy, hard guards, and logs now live under `<agentDir>/my-pi/permission-system/` instead of `<agentDir>/extensions/pi-permission-system/`; the bundle's install/update scripts delete and redeploy that whole directory on every run, so the extension itself never seeds or migrates configuration. Files left at the old location are ignored.
 
 ### Removed