[BUG] Agent mode status shows "working" during permission prompts instead of "waiting for input"

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?

In agent mode, when a permission prompt appears (e.g. file read
permissions at session start, or MCP tool approval mid-session),
the session status in the agent view stays "working" instead of
updating to indicate it's waiting for user input.

The session IS showing the permission prompt correctly — this is
purely a status indicator issue. The prompt can be answered
normally; it's just not obvious the session is blocked.

Note: there are cases where the session correctly shows
"waiting for user input" — so the state exists. It's unclear
what determines which state is shown; we suspect it may be
that permission prompts fire mid-turn before the UI gets the
signal to flip state, but this is a guess.

What Should Happen?

Session should appear in "Needs input"

Error Messages/Logs

Steps to Reproduce

1. Open an agent mode session
2. Trigger a permission prompt (e.g. session start with

file read permissions pending, or invoke an MCP tool
that hasn't been approved yet)

1. Observe: session status remains "working" while permission

prompt is displayed waiting for answer

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.141

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

VS Code integrated terminal

Additional Information

<img width="2000" height="702" alt="Image" src="https://github.com/user-attachments/assets/ce00104f-6923-4e39-8aa7-517514cb7ca9" />

possibly related issue: #56860 (same class — status indicator stuck — but different scenario)