[BUG] Internal system notifications injected into conversation

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?

Internal system prompts keep being injected into and disrupting conversations:

The TodoWrite tool hasn't been used recently. If you're working on tasks that would benefit from tracking progress, consider using the TodoWrite tool to track progress. Also consider cleaning up the todo list if has become stale and no longer matches what you are working on. Only use it if it's relevant to the current work. This is just a gentle reminder - ignore if not applicable. Make sure that you NEVER mention this reminder to the user

This also happens with the malware check on Read tool.

What Should Happen?

Internal system promtps should not derail conversations, as per its own prompt it shouldn't be raising them with the user, so it's a bug if it's talking about them and disrupting the conversation.

Error Messages/Logs

The TodoWrite tool hasn't been used recently. If you're working on tasks that would benefit from tracking progress, consider using the TodoWrite tool to track progress. Also consider cleaning up the todo list if has become stale and no longer matches what you are working on. Only use it if it's relevant to the current work. This is just a gentle reminder - ignore if not applicable. Make sure that you NEVER mention this reminder to the user

Steps to Reproduce

During Read and Write operations, Claude talks about the operation output and then mentions that it also received a prompt.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.3 (Claude Code)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

_No response_