[BUG] Default custom agent in VSCode extension is ignoring the "tool" directive

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?

Custom agents can restrict what tools are used when running them using the "tools" setting in the agent frontmatter definition (see https://code.claude.com/docs/en/sub-agents#available-tools).

When specifying a default agent in ~/.claude/settings.json and running this agent in the VSCode extension, the tools definition is ignored and all tools are exposed to the LLM

What Should Happen?

Only the tools listed in the "tools" section of the agent frontmatter should be exposed to the LLM

Error Messages/Logs

Steps to Reproduce

1. Create a new custom agent, my-agent.md

---
name: my-agent
description: You are a custom agent
model: inherit
tools: Skill
---
Some description

1. In ~/.claude/settings.json add this line:

  "agent": "my-agent.md",

1. Start the VSCode with the extension
2. Type a message in the Claude Code extension and send it
3. Observe that the tool definition in the anthropic message definition sent to the LLM contains all tools instead of just the "Skill" tool

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.89

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

VS Code integrated terminal

Additional Information

This works as expected in the CLI version of Claude Code

We also tried adding the additional line

disallowedTools: Agent, Edit, Write, Read, Grep, Glob

into the frontmatter but that also did not prevent the tools from adding to the context