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

pi-tool-search/CHANGELOG.md

@@ -18,6 +18,10 @@
 - Added the authoritative `user-interaction` group for the maintained `ask_user_question` TUI tool.
 - Added authoritative `chrome-navigation`, `chrome-interaction`, and `chrome-debugging` groups for all 21 tools registered by the pinned `pi-chrome` bridge after explicit session authorization.
 - Raised the bundle defaults to five active groups and 28 dynamic tools, and pinned the high-frequency Context Mode execution trio alongside CodeGraph exploration and LSP diagnostics.
+- Moved user configuration from the `settings.json` `toolSearch` section to the bundle-owned `<agent-dir>/my-pi/tool-search/config.json`, deployed by the bundle's rebuild script; a missing or invalid file falls back to `BUNDLE_TOOL_SEARCH_DEFAULTS`. Moved the model-enriched catalog cache to `<agent-dir>/my-pi/tool-search/catalog-v1.json`.
+
+### Removed
+- Removed `ensureToolSearchDefaults`, `BUNDLE_TOOL_SEARCH_DEFAULTS_VERSION`, `bundleDefaultsVersion` handling, and all `settings.json` reads/writes; the bundle deploys config via `scripts/rebuild-bundle-config.mjs` instead of extension-side seeding or snapshot migration.
 - Pinned all six Hermes memory tools in the bundle defaults and raised `bundleDefaultsVersion` to 3. The injected memory policy expects these schemas every turn, and pinning also keeps the request prefix cache-stable instead of paying a `tool_search` round trip plus a cache invalidation. `scripts/migrate-tool-search-settings.mjs` migrates the complete version-2 snapshot with an owner-only backup, atomic replacement, and fail-safe preservation of custom or invalid settings.
 - Pinned `context_tree_query` alongside the memory tools and raised `bundleDefaultsVersion` to 4. Recovering pruned tool evidence must not depend on a `tool_search` activation, and the added name keeps the request prefix stable. The migration helper now accepts the complete version-3 snapshot in addition to version 2.
 - Added atomic multi-group activation through `tool_search.groups`, bounded to five exact group ids and rejected without state changes when the complete workflow cannot fit.