UserPromptSubmit hooks not fired when user sends message mid-turn (regression)

Description

UserPromptSubmit hooks are completely skipped when the user sends a message while the agent is actively generating (mid-turn). The message is delivered to the agent as an interrupt, but no hooks fire. This appears to be a regression — it previously worked.

Steps to reproduce

1. Configure a UserPromptSubmit hook (command or HTTP type):

{
  "hooks": {
    "UserPromptSubmit": [{
      "hooks": [{
        "type": "http",
        "url": "http://127.0.0.1:9801/UserPromptSubmit",
        "timeout": 180000
      }]
    }]
  }
}

1. Start a session and give the agent a long-running task (e.g., reading multiple files)
2. While the agent is working (mid-turn, making tool calls), type and send a new message
3. Observe: the message appears as an interrupt to the agent, but UserPromptSubmit hooks never fire

Evidence

Server-side logging on the hook HTTP endpoint shows:

• Normal prompts (agent idle): HTTP BATCH UserPromptSubmit:* appears in logs, all hooks execute
• Mid-turn messages: Zero UserPromptSubmit entries in logs. Only PreToolUse and PostToolUse batches continue from the current turn

The message is delivered to the agent via a <system-reminder> containing "The user sent a new message while you were working: ..." — but this bypasses all hook processing.

Impact

Any functionality that relies on UserPromptSubmit silently fails for mid-turn messages:

• Prompt parsing (e.g., extracting structured task commands from user input)
• Intent classification (determining if user wants investigation vs. implementation)
• Context injection (attaching external data/queue events to the prompt)
• Prompt validation/gating (blocking or modifying prompts before the agent sees them)

This is particularly problematic because users naturally send follow-up instructions while the agent is working. All hook-based processing for these messages is lost.

Expected behavior

UserPromptSubmit hooks should fire for every user-submitted message, regardless of whether the agent is idle or mid-turn. The hook output (additionalContext, systemMessage, etc.) should be attached to the message when it's delivered to the agent.

Environment

• Claude Code version: 2.1.69
• Platform: Windows 11 + WSL2
• Hook type tested: HTTP (type: "http")