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/README.md

@@ -34,7 +34,7 @@ pi install npm:@gotgenes/pi-permission-system
 
 ## Quick Start
 
-1. Create ordinary policy at `~/.pi/agent/extensions/pi-permission-system/policy.jsonc`:
+1. Create ordinary policy at `~/.pi/agent/my-pi/permission-system/policy.jsonc`:
 
     ```jsonc
     {
@@ -51,7 +51,7 @@ pi install npm:@gotgenes/pi-permission-system
     }
     ```
 
-2. Create independent hard guards at `~/.pi/agent/extensions/pi-permission-system/hard-guards.jsonc`:
+2. Create independent hard guards at `~/.pi/agent/my-pi/permission-system/hard-guards.jsonc`:
 
     ```jsonc
     {
@@ -86,12 +86,12 @@ The integrated extension uses two independent global JSONC files:
 
 | Purpose | Scope | Path |
 | ------- | ----- | ---- |
-| Ordinary policy, runtime knobs, AutoReview | Global only | `~/.pi/agent/extensions/pi-permission-system/policy.jsonc` |
-| Non-overridable hard guards | Global only | `~/.pi/agent/extensions/pi-permission-system/hard-guards.jsonc` |
+| Ordinary policy, runtime knobs, AutoReview | Global only | `~/.pi/agent/my-pi/permission-system/policy.jsonc` |
+| Non-overridable hard guards | Global only | `~/.pi/agent/my-pi/permission-system/hard-guards.jsonc` |
 
 Project-level `policy.jsonc` files are ignored. Project agent Markdown remains a separate per-agent restriction mechanism.
 
-The bundle seeds missing files with mode `0600`. During `update.sh`, only the exact known legacy default policy is backed up and replaced by the current bundled seed. Any customized or invalid policy is preserved and reported instead of being guessed or overwritten.
+The bundle deploys both files with mode `0600` via `scripts/rebuild-bundle-config.mjs`: every `install.sh` / `update.sh` run rebuilds the whole `<agentDir>/my-pi/` tree, overwriting local edits without a backup — keep durable changes in the repository's `config/` sources. Files left at the former `extensions/pi-permission-system/` location are ignored.
 
 Within a pattern map, the most specific match wins: exact patterns, then more literal characters, fewer wildcards, and longer patterns. Declaration order is only a tie-breaker.