[BUG] `--json-schema` defined JSON doesn't exist in `structured_output`

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?

I'm using claude code to run a custom slash command:

claude --dangerously-skip-permissions --output-format json --json-schema "$(cat ./schema.json)" --append-system-prompt "$(cat ./prompt.md)" -p "/my-command"

Based on the document the result json should include field structured_output with the json object defined by the schema. But what I got is a json without structured_output. Instead, the json includes field result which is a markdown string include the json object expected.
And unfortunately, sometimes the json in the markdown doesn't follow the definition in the schema. In my case, there is a field in the json expect the value is a number, which is extracted from a string. I guess this is because the prompt explains how to extract the data for the json.

One example what I got:

{
  "type": "result",
  //...
  "result": "xxx\n```json\n{\n\"key\": \"value\"\n}\n```"
}

What Should Happen?

In the result json, the schema defined json object should exist in structured_output field. For example:

{
  "type": "result",
  //...
  "structured_output": {
    // the json content defined by the schema
  }
}

Error Messages/Logs

Steps to Reproduce

1. Define a json schema and a prompt to describe how to get the values required by the json schema
2. Call claude with `-p --output-format json --json-schema $(cat ./schema.json) --append-system-prompt $(cat ./prompt.md) "query"

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.0.76

Claude Code Version

2.1.1

Platform

Google Vertex AI

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_