chore: Pi 开发依赖跟随最新版并去掉测试里的固定版本号

- pi-hermes-memory / pi-notify / pi-permission-system / pi-subagents 的
  @earendil-works/* devDependencies 改为 latest，pi-rtk-optimizer 放开
  peer 范围；各子包锁文件刷新到 Pi 1.3.0，测试改为验证当前宿主 API。
- 新增 scripts/update-pi-devdeps.sh，统一刷新根与子包锁文件中的 Pi 版本。
- pi-subagents 适配 Pi 1.3：mention clone 改走 systemPromptOverride、
  BOM frontmatter、e2e 读取规范化后的 system 消息与工具列表。
- 根测试不再写死 ssh2 / jiti / better-sqlite3 / context-mode 版本号，
  改为精确版本格式与锁文件一致性断言；新增 latest 约束测试。

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

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

pi-subagents/test/mention-clone.test.ts

@@ -17,10 +17,14 @@ import { beforeEach, describe, expect, it, vi } from "vitest";
 
 // Hoisted: vi.mock's factory is lifted above the imports, so it cannot close
 // over ordinary top-level consts.
-const { buildSessionContext, createAgentSession, inMemory } = vi.hoisted(() => ({
+const { buildSessionContext, createAgentSession, inMemory, loaderOptions } = vi.hoisted(() => ({
   buildSessionContext: vi.fn(),
   createAgentSession: vi.fn(),
   inMemory: vi.fn(),
+  // The clone's prompt reaches the session through the loader's
+  // systemPromptOverride (Pi 1.3 made AgentState.systemPrompt read-only), so
+  // capture what runMentionClone hands DefaultResourceLoader.
+  loaderOptions: { current: undefined as Record<string, unknown> | undefined },
 }));
 
 vi.mock("@earendil-works/pi-coding-agent", async () => {
@@ -29,6 +33,12 @@ vi.mock("@earendil-works/pi-coding-agent", async () => {
     ...actual,
     buildSessionContext,
     createAgentSession,
+    DefaultResourceLoader: class extends actual.DefaultResourceLoader {
+      constructor(options?: Record<string, unknown>) {
+        loaderOptions.current = options;
+        super(options);
+      }
+    },
     SessionManager: { ...actual.SessionManager, inMemory },
   };
 });
@@ -44,6 +54,7 @@ const CONVERSATION = [
 
 beforeEach(() => {
   createAgentSession.mockReset();
+  loaderOptions.current = undefined;
   inMemory.mockReset();
   inMemory.mockReturnValue({ kind: "in-memory-session-manager" } as any);
   buildSessionContext.mockReset();
@@ -104,6 +115,13 @@ function cloneSession(turn?: (tool: any) => Promise<void> | void) {
     dispose: vi.fn(),
   } as any;
   createAgentSession.mockImplementation(async (opts: any) => {
+    // What the real wiring does: the loader's systemPromptOverride rewrites the
+    // rebuilt base before the session's state gets it.
+    const override = loaderOptions.current?.systemPromptOverride as
+      | ((base: string | undefined) => string | undefined)
+      | undefined;
+    const overridden = override?.(session.agent.state.systemPrompt);
+    if (overridden !== undefined) session.agent.state.systemPrompt = overridden;
     const tools = visibleTools(opts);
     session.prompt.mockImplementation(async () => {
       // No tool, no tool call: the model can only answer in prose.