chore: 清理 pi-mcp-adapter 移除后的陈旧引用

Pi 0.99+ 已内置 MCP（builtin:mcp），组合包不再加载 adapter；
删除引用不存在 mcp 工具的 mcp-management 分组，并把权限文档
中的 MCP 表述澄清为内置 mcp__<server>__<tool> 命名。

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pi-permission-system/docs/configuration.md

@@ -432,6 +432,8 @@ To deliberately opt into permissive bash, set `"bash": { "*": "allow" }` explici
 
 ### `mcp` Surface
 
+The `mcp` surface applies to a unified proxy tool named `mcp` (e.g. `pi-mcp-adapter`) whose input carries `tool`/`server`/`connect`/`describe`/`search` fields. Pi's built-in MCP (0.99+) instead exposes each server tool as a first-class `mcp__<server>__<tool>` tool — gate those with ordinary tool-name rules such as `"mcp__myServer__*": "ask"`, not this surface.
+
 MCP permissions match against derived targets from tool input:
 
 | Target type       | Examples                                                              |
@@ -486,7 +488,7 @@ Skill name patterns use `*` and `?` wildcards (note: surface is `skill`, not `sk
 
 ### `path` Surface
 
-Cross-cutting gate that applies to **all** file access — built-in Pi tools (`read`, `write`, `edit`, `find`, `grep`, `ls`), bash commands, MCP calls (via `input.arguments.path`), and extension tools (via `input.path` or a registered access extractor).
+Cross-cutting gate that applies to **all** file access — built-in Pi tools (`read`, `write`, `edit`, `find`, `grep`, `ls`), bash commands, `mcp` proxy calls (via `input.arguments.path`), and extension tools (via `input.path` or a registered access extractor).
 A `path` deny cannot be overridden by a per-tool allow.
 Extension and MCP path tools are gated by default — no registration needed — so a `path` deny protects sensitive files from every path-aware tool, not just the built-in six.