[BUG] CLI does not emit can_use_tool control_request when --permission-prompt-tool stdio

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

When the CLI is run with --permission-prompt-tool stdio (e.g. by the Python Agent SDK when can_use_tool is set), it never sends control_request events with subtype can_use_tool before executing tools. Tool use succeeds (e.g. Write creates the file), but the parent process (SDK) never receives a permission request, so permission callbacks never run.

Observed Behavior: No permission request is emitted. The CLI runs the tool and continues; the SDK’s can_use_tool callback is never invoked.

Impact: Human-in-the-loop or other permission flows that rely on the control protocol cannot work when the SDK drives the CLI with permission_prompt_tool_name="stdio".

Environment: CLI 2.1.73 + 2.1.74 (Claude Code), Python SDK 0.1.48. Same behavior reported on other versions (see linked SDK issue).

Related: https://github.com/anthropics/claude-agent-sdk-python/issues/469 (tracking the symptom from the SDK side; the fix likely belongs in the CLI).

What Should Happen?

Before running a tool, the CLI sends a control_request with subtype can_use_tool over the control channel and waits for a control_response (allow/deny) from the parent.

Error Messages/Logs

Steps to Reproduce

1. Use the Python SDK to run the Claude Code CLI (e.g. run() or equivalent that spawns the CLI subprocess).
2. Set permission_mode="default" and pass a can_use_tool callback that logs or prints when invoked.
3. Send a prompt that causes the model to use a tool (e.g. “Create a file called test.txt with hello inside”).
4. Expected: Callback runs before the tool executes. Actual: Callback never runs; the tool runs and the run completes without any callback invocation.

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.74

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

WSL (Windows Subsystem for Linux)

Additional Information

_No response_