[BUG] Plan Mode → Escape → Manual Mode: agent ignores STOP and keeps running workers until full process kill

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 Claude Code is in Plan Mode and the operator presses Escape to interrupt it, then resets the session back to Manual Mode and issues a "STOP" prompt, Claude Code does not stop. Instead:
• Background workers/tool calls keep running as if still in Auto Mode
• The session stops accepting new prompts — subsequent "STOP" messages are ignored
• The mode indicator may show Manual Mode, but actual execution behavior does not match it
• CLAUDE.md explicitly documents the expected STOP behavior for this scenario, and it is not honored (Please see attached file)

What Should Happen?

CLAUDE.md Once reset to Manual Mode and given a STOP instruction (per CLAUDE.md), Claude Code should immediately halt all running workers/tool execution and accept new prompts. Please NOTE: "Sometimes, this works, but more times that not, Claude Code Ignores Prompts and continues to work as if it is in Auto Mode instead of Reading and acting on the Prompts.

Error Messages/Logs

Claude is not reporting stack traces like when I was using Copilot Front-ending Claude Opus 4.6/4.7 before I received my Anthropic License.

Steps to Reproduce

1. Start a session with Claude Code integrated via the Visual Studio Enterprise 2026 extension Claude=>Claude CLI
2. Enter Plan Mode
3. Ask Claude Opus 4.8 to Produce a plan for a specific functional change we are working on and instruct it to Save the plan to an explicit file (fix-this-bug-plan.md) file and then STOP and wait for me to review it.
4. This happens as requested, I review it and Claude is put in Auto-Mode and starts working. As I’m reviewing the steps taken, I realize that I missed something in the plan review or Claude Opus is doing something unanticipated.
5. Press Escape to interrupt Claude mid-response
6. Reset the session to Manual Mode
7. Send a prompt containing "STOP"
8. Observe: workers continue running, further prompts are not accepted, execution continues as if Auto Mode were still active
9. Sometimes I can finally get it to stop, but now we are in NOT in Auto Mode anymore, so I keep in Manual Mode and try to explain what went wrong and why things need to change. This last time I told it to write an entire new plan and to throw away the plan it was working on because of a fundamental misunderstanding. And it responses that it understood to problem / issue and will write a new plan to address it and its initial outline of what it says is going to go into the plan looks fine, however, this is where things fall off the Rails! Instead of completing the plan, saving it and telling me where it saved it, it just asks me if I want it to go into Auto-Mode and start working on it.
10. I realize it has not actually produced a plan anywhere I can read it, so I prompt it to first STOP!!! STOP!!! Please save the plan you are working on to @docs/plans/new-plan-name.md and STOP!! And let me review it.
11. Claude Code takes off running on the “yet to be reviewed or even viewed plan” and lists the first worker step it is working one. I immediately escape and tell it to STOP! It just keeps running! At this point I escape it and put it into Manual Mode again and it says that it is waiting for 3 workers to finish, or something like that, at which point, I just restart the session, exist Visual Studio 2026, stop the Claude window app and bring up Task Manager and finally manage to terminate all 9 running Claude Processes that did NOT STOP!

Expected Behavior
Once reset to Manual Mode and given a STOP instruction (per CLAUDE.md), Claude Code should immediately halt all running workers/tool execution and accept new prompts.
Actual Behavior
Session becomes unresponsive to STOP and further input. The only recovery path found:

1. Kill all Claude processes
2. Exit Visual Studio 2026 Enterprise
3. Exit and restart the Windows Desktop Claude app
4. Relaunch Visual Studio 2026

Environment
• IDE: Visual Studio 2026 Enterprise
• Integration: Claude Code extension
• OS: Windows 11 x64 up to date OS patch levels… our company watches this closely and forces upgrades as soon as the come out for both the OS and Visual Studio Enterprise!
• CLAUDE.md: contains explicit STOP-on-manual-mode instruction (see attached)

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

This worked much better, but not perfectly in Claude 4.6 when I started the current project, but to me this looks like a core problem that is the lack of a safety gate operation when Running Modes are changed!

Claude Code Version

2.1.207 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

This is not a work stopped failure because it can not continue. It is a STOP, before you do any more damage problem! This also results in the rolling back of code and is very costly from a Token standpoint, because I literally know the work that Claude is attempting will have to be redone and it is just consuming tokens like made "thinking" it has gotten approval to work, when it clearly has not!