User messages during tool execution are displayed in system-reminder tags, making them easy to overlook

Problem

When a user sends a message while a tool (Bash, Read, Glob, etc.) is being executed, that message appears inside <system-reminder> tags alongside the tool results.

This causes a serious UX issue: user messages like "stop" or "wait, I have more information" are visually grouped with automated system notifications, making them easy to overlook or dismiss.

Reproduction Steps

1. User initiates a task that requires multiple tool calls
2. While Claude is executing tools, user sends a message (e.g., "stop" or "I have more to say")
3. The user's message appears in <system-reminder> tags within the tool result output
4. Claude may continue executing tools, treating the user message as a low-priority system notification

Expected Behavior

User messages should be clearly distinguished from system-generated reminders. They should either:

• Interrupt tool execution immediately
• Be displayed in a separate, prominent format that cannot be confused with automated notifications

Actual Behavior

User messages are wrapped in the same <system-reminder> tags used for automated notifications (like TodoWrite reminders), making them indistinguishable from system-generated content.

Impact

• Users feel ignored when their messages are not acknowledged
• Important user instructions ("stop", "wait", corrections) may be missed
• Trust in the assistant is damaged when user input is overlooked