[BUG]

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?

When using CLAUDE_CONFIG_DIR env variable to maintain separate Claude profiles, the profile using a non-standard directory does not have access to user level MCPs (outside of the claude.ai managed ones).

I can define project level MCPs but this is tedious for more than one off use cases.

What Should Happen?

Claude, ideally, would allow for mcps to be defined in the ~/<CLAUDE_CONFIG_DIR>/settings.json file.
Alternatively, if finer grained control is not implemented, mcps defined in ~/.claude.json would be respected in all instances and configurations.

Error Messages/Logs

Steps to Reproduce

1. Have an existing Claude profile and user scoped MCPs.
2. Start a claude code instance with a different config directory already created, ~/.claude-demo for this example. CLAUDE_CONFIG_DIR=~/.claude-demo claude
3. check your available mcps using /mcp

Claude Model

Not sure / Multiple models

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.195 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other

Additional Information

_No response_