Add a script host, deferred tools, and background MCP connect

Why: models need a capped way to call several tools from one script, and a slow MCP server must not block the first prompt.
Evidence: GOWORK=off go test ./runtime/codeorch/ ./runtime/tools/ ./runtime/mcp/ ./runtime/policy/ ./adapters/native/
Impact: run_tool_script stays unregistered until the caller turns it on. Deferred tools stay out of the model list. An unready MCP server connects in the background.
Refs: feature/code-orchestration
Co-authored-by: Cursor <cursoragent@cursor.com>

adapters/native/backend.go

@@ -49,6 +49,8 @@ type ToolOptions struct {
 	HostTools        []tools.Tool
 	Checkpoints      *checkpoint.Log
 	CheckpointAnchor func() string
+	// CodeOrchestration 为真时注册 run_tool_script。默认关。
+	CodeOrchestration bool
 }
 
 // SessionOptions 是单次执行的会话预算与压缩。
@@ -73,6 +75,8 @@ type GateOptions struct {
 	Reminders   func(turn int) []string
 	RepeatGuard bool
 	Hooks       *hooks.Bus
+	// Ask 在 MCP 工具要求用户输入时调用。nil 则把问题作为错误返回。
+	Ask func(ctx context.Context, question string) (string, error)
 }
 
 // Options 构造后端所需的模型接入与执行参数（由组合根注入，无产品依赖）。
@@ -147,6 +151,9 @@ func (b *Backend) Execute(ctx context.Context, req exec.Request) (*exec.Result,
 	if b.opts.Stream == nil && (strings.TrimSpace(b.opts.APIBase) == "" || strings.TrimSpace(b.opts.APIKey) == "") {
 		return &exec.Result{Success: false, ErrorReason: "agent-native backend requires api base/key (or injected stream)"}, nil
 	}
+	if b.opts.Ask != nil {
+		ctx = mcp.WithAsk(ctx, b.opts.Ask)
+	}
 	model := strings.TrimSpace(b.opts.Model)
 	if strings.TrimSpace(req.Model) != "" {
 		model = strings.TrimSpace(req.Model)
@@ -204,9 +211,19 @@ func (b *Backend) Execute(ctx context.Context, req exec.Request) (*exec.Result,
 			}
 			tools.RegisterExecTools(reg, workDir, execCfg)
 		}
+		if b.opts.CodeOrchestration {
+			tools.RegisterCodeTool(reg)
+		}
+		reg.SetActivationFile(filepath.Join(workDir, ".agentx", "activated-tools.json"))
+		_ = reg.RestoreActivated()
 		if b.opts.MCP != nil {
-			if err := b.opts.MCP.RegisterInto(ctx, reg); err != nil {
-				return &exec.Result{Success: false, ErrorReason: err.Error()}, nil
+			switch {
+			case len(req.ToolAllowlist) > 0 || b.opts.MCP.Ready():
+				if err := b.opts.MCP.RegisterInto(ctx, reg); err != nil {
+					return &exec.Result{Success: false, ErrorReason: err.Error()}, nil
+				}
+			default:
+				b.opts.MCP.StartBackground(ctx, reg)
 			}
 		}
 		subagent.Register(reg, b.opts.Subagent)

adapters/native/exec_tools_test.go

@@ -212,6 +212,9 @@ func TestBackendMCPToolsWiredViaOptions(t *testing.T) {
 		t.Fatal(err)
 	}
 	defer mgr.Close()
+	if err := mgr.RegisterInto(context.Background(), tools.NewRegistry(t.TempDir())); err != nil {
+		t.Fatal(err)
+	}
 	stream, c := captureStream(
 		llm.Message{Role: llm.RoleAssistant, StopReason: llm.StopToolCalls, ToolCalls: []llm.ToolCall{{
 			ID: "c1", Name: "mcp__fake__echo", Arguments: `{"text":"via-backend"}`,