[BUG] SDK doesn't read project level MCPs or Slash Commands for new queries

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 have project level MCPs defined in my .mcp.json file and a few slash commands added under my projects .claude/commands directory. Upon launching the Claude Agent SDK from that directory, Claude doesn't seem to have access to either the MCP servers or slash commands defined in these project-level files.

This can be verified by calling the supportedCommands() and mcpServerStatus() callbacks after launching the SDK. They don't return project-level MCPs/commands.

Note: These methods DO however return user-level MCPs and Slash Commands under the same situation.

What Should Happen?

The Claude Agent SDK (just as the CLI) should read from the .mcp.json file and .claude/commands directory in my current working directory upon startup.

Error Messages/Logs

Steps to Reproduce

1. Create a .mcp.json file in your current working directory.
2. Create a command under .claude/commands in your current working directory.
3. Run the query() function with an AsyncIterable prompt in the Claude Agent SDK.
4. Call the mcpServerStatus() and supportedCommands callbacks
5. Verify that the results do not contain project level MCPs and slash commands

Claude Model

None

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.0.76

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Non-interactive/CI environment

Additional Information

A similar issue was opened earlier this month but the issue does not seem to have been resolved.
Previous Issue: https://github.com/anthropics/claude-code/issues/13107