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/troubleshooting.md

@@ -6,7 +6,7 @@
 | ----------------------------------------------------------------- | ----------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
 | Config not applied (everything asks)                              | File not found or parse error                                     | Verify the global policy at `~/.pi/agent/my-pi/permission-system/policy.jsonc` (respects `PI_CODING_AGENT_DIR`); check JSONC syntax |
 | Per-agent override not applied                                    | Frontmatter parsing issue                                         | Ensure `---` delimiters at file top; keep YAML simple; restart session                                                                            |
-| Tool blocked as unregistered                                      | Unknown tool name                                                 | Use a registered `mcp` tool for server tools: `{ "tool": "server:tool" }`                                                                         |
+| Tool blocked as unregistered                                      | Unknown tool name                                                 | Server tools arrive as `mcp__<server>__<tool>` under Pi's built-in MCP (check `/mcp`); a unified `mcp` proxy tool uses `{ "tool": "server:tool" }` |
 | `/skill:<name>` blocked                                           | Deny policy or confirmation unavailable                           | Check merged `skill` policy (global/project/agent layers). `ask` still requires UI or forwarded confirmation.                                     |
 | External file path blocked                                        | `external_directory` is `ask` without UI or `deny`                | Allow/ask the permission or keep file tools inside the active working directory.                                                                  |
 | Spurious external-path prompt for `cd <subdir> && grep … ../path` | Relative path was resolved against cwd instead of the `cd` target | Fixed in current version — paths after a leading `cd <subdir> &&` are resolved against the cd target, matching actual shell behavior.             |