Assistant responses appear above user messages, breaking dialog chronology

Description

During a conversation, assistant responses intermittently appear above the user's messages instead of below them. This breaks the chronological order of the dialog and makes the interaction confusing.

Steps to Reproduce

1. Have an active conversation with Claude Code CLI
2. Send messages while system-reminder hooks are firing (e.g., file-change notifications or stop hooks)
3. Observe that some assistant responses render above the user's subsequent messages

Expected Behavior

Assistant responses should always appear in chronological order — below the user message they are responding to.

Actual Behavior

Responses appear displaced upward in the conversation, sometimes rendering above later user messages. The dialog flow becomes non-linear and hard to follow.

Possible Cause

System-reminder hooks (e.g., file-change notifications, stop hook callbacks) seem to interleave between user and assistant messages, potentially causing display order issues.

Environment

• Claude Code CLI
• macOS (Darwin 25.3.0)
• Model: claude-opus-4-6