[BUG] --append-system-prompt does not append to the system prompt, but is a user message instead

Environment

• Platform (select one):
• [ ] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [x] Other: Claude Code via Max 20 subscription
• Claude CLI version: 1.0.61
• Operating System: MacOS
• Terminal: Alacritty

Bug Description

--append-system-prompt does not actually append to the system prompt, but injects a user message instead. This completely defeats the purpose of it being a system prompt: the context is lost over time, and may even be subject to compaction, which would lead to complete loss of the role.

Steps to Reproduce

1. Use --append-system-prompt
2. Observe with mitmproxy that it is actually a <user> message

Expected Behavior

It would be appended as-is after the existing claude code system prompt, perhaps with some clear markers around it.

Actual Behavior

It is sent as a user message.

Additional Context

<img width="1263" height="494" alt="Image" src="https://github.com/user-attachments/assets/346ad22b-0415-4b41-85bd-3921713c7824" />

Here you can see that the literal text I provided as --append-system-prompt is actually provided as a user message, which makes it not very much different than just a custom slash command and defeats the purpose.