feat: codegraph_explore 改为原生 CLI 工具并移除 /plugin_init

codegraph 有一等公民 CLI 且上游保证其输出与 codegraph_explore MCP
工具一致，走共享 MCP adapter 只是多余的传输层。改为原生 Pi 工具后
每次调用以短命 codegraph explore 进程完成，去掉常驻 server/daemon；
未初始化项目经 ctx.ui.confirm 确认后 init 并自动重试，拒绝或失败时
打回并引导模型回退 find/grep/read/LSP；结果按 codegraph.db mtime
做有界缓存，索引一变即失效。共享 MCP adapter 只保留 Exa；工具名
不变，权限策略、Tool Search 常驻表、路由规则与分组不受影响。

Generated with [Devin](https://devin.ai)

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

tests/mcp.test.ts

@@ -4,7 +4,7 @@ import test from "node:test";
 
 import { createMcpConfig, EXA_TOOLS } from "../extensions/mcp-config.ts";
 
-test("one MCP adapter config contains both Exa and CodeGraph", () => {
+test("the shared MCP adapter config only connects Exa", () => {
 	assert.deepEqual(createMcpConfig({}), {
 		settings: {
 			disableProxyTool: true,
@@ -21,16 +21,6 @@ test("one MCP adapter config contains both Exa and CodeGraph", () => {
 				approveTools: false,
 				exposeResources: false,
 			},
-			codegraph: {
-				command: "codegraph",
-				args: ["serve", "--mcp"],
-				lifecycle: "keep-alive",
-				directTools: ["codegraph_explore"],
-				includeTools: ["codegraph_explore"],
-				toolPrefix: "none",
-				approveTools: false,
-				exposeResources: false,
-			},
 		},
 	});
 });