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/extension-load.test.ts

@@ -32,8 +32,13 @@ test("all package extensions load together without global registration conflicts
 		allowScripts: Record<string, boolean>;
 	};
 	assert.ok(
+		packageJson.pi.extensions.includes("./extensions/codegraph.ts"),
+		"the bundle must expose the native codegraph_explore tool",
+	);
+	assert.equal(
 		packageJson.pi.extensions.includes("./extensions/plugin-init.ts"),
-		"the bundle must expose the project plugin initializer command",
+		false,
+		"the retired plugin initializer command must not be loaded",
 	);
 	assert.ok(
 		packageJson.pi.extensions.includes("./pi-hermes-memory/src/index.ts"),