[BUG] MCPs can only be seen from the directory you are in when they are added even though they are in the global config

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?

MCP Server Detection Bug Report

Summary

Global MCP servers configured in ~/.claude/mcp_config.json are detected and work in one directory (fs-ci) but not in another (mobile-ios), even though both directories use the same global configuration file.

Environment

Claude Code Version: 2.1.7

System Information:

• OS: macOS 26.2 (Build 25C56)
• Kernel: Darwin 25.2.0
• Architecture: ARM64 (Apple Silicon)
• Node.js: v25.2.1
• npm: 11.7.0

Configuration

Global MCP Configuration

Location: ~/.claude/mcp_config.json

{
  "mcpServers": {
    "atlassian": {
      "command": "mcp-remote",
      "args": [
        "https://mcp.atlassian.com/v1/mcp"
      ]
    },
    "github": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-github"
      ],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "[REDACTED]"
      }
    }
  }
}

File Permissions: -rw-r--r-- (readable by all)

Local Project Configurations

mobile-ios: .claude/settings.local.json

{
  "permissions": {
    "allow": [
      "Bash(find:*)",
      "Bash(chmod:*)",
      "Bash(./replace_person_manager_calls.sh:*)",
      "mcp__XcodeBuildMCP__discover_projs",
      "mcp__XcodeBuildMCP__list_schemes",
      "mcp__XcodeBuildMCP__list_sims",
      "mcp__XcodeBuildMCP__boot_sim",
      "mcp__XcodeBuildMCP__open_sim",
      "mcp__XcodeBuildMCP__build_sim",
      "mcp__XcodeBuildMCP__clean",
      "mcp__XcodeBuildMCP__get_sim_app_path",
      "mcp__XcodeBuildMCP__get_app_bundle_id",
      "mcp__XcodeBuildMCP__install_app_sim",
      "mcp__XcodeBuildMCP__launch_app_logs_sim",
      "mcp__XcodeBuildMCP__screenshot",
      "mcp__XcodeBuildMCP__stop_sim_log_cap",
      "Bash(./extract_and_chunk_pdf.sh:*)",
      "Bash(brew list:*)",
      "Bash(brew install:*)",
      "Bash(python3:*)",
      "Bash(swift build)",
      "Bash(xcodebuild:*)",
      "WebFetch(domain:beta.familysearch.org)",
      "Skill(local-persistence)"
    ],
    "deny": [],
    "ask": []
  }
}

fs-ci: .claude/settings.local.json

{
  "permissions": {
    "allow": [
      "Bash(find:*)",
      "mcp__atlassian__atlassianUserInfo",
      "mcp__atlassian__search",
      "mcp__atlassian__searchJiraIssuesUsingJql"
    ]
  }
}

Observed Behavior

Working Directory: /Users/rickmeier1/sb/fs-ci

$ claude mcp list
Checking MCP server health...

atlassian: https://mcp.atlassian.com/v1/mcp (HTTP) - ✓ Connected
github: npx -y @modelcontextprotocol/server-github - ✓ Connected

✅ Result: Both MCP servers detected and connected successfully

Working Directory: /Users/rickmeier1/sb/mobile/mobile-ios

$ claude mcp list
No MCP servers configured. Use `claude mcp add` to add a server.

❌ Result: No MCP servers detected, despite using the same global config

Repository Context

Both directories are git repository roots:

• mobile-ios: iOS multi-app repository
• fs-ci: CI/CD repository

Both have local .claude/ directories with settings.local.json files, but neither contains any local MCP configuration files (no mcp_config.json at project level).

Expected Behavior

The global MCP configuration in ~/.claude/mcp_config.json should be detected and used consistently across all directories. The claude mcp list command should show the same MCP servers (atlassian and github) in both directories.

Actual Behavior

The global MCP configuration is only detected in some directories but not others, despite there being no local MCP configuration that would override the global settings.

Potential Issues

1. Directory-specific MCP detection logic: Something about the mobile-ios directory prevents global MCP config discovery
2. Local settings interference: The presence of different local permissions in settings.local.json might affect MCP detection
3. Caching issue: MCP server list might be cached per-project and not refreshing
4. Project initialization: The mobile-ios project might need some form of initialization to recognize global MCPs

Workarounds Attempted

None successful - the issue persists across sessions.

Additional Notes

• The permissions in mobile-ios/.claude/settings.local.json reference mcp__XcodeBuildMCP__*, but this MCP is not configured in the global config
• The .claude/ directory structure differs slightly between projects (mobile-ios has agents/ and skills/ subdirectories)
• No local mcp_config.json exists in either project directory

Reproduction Steps

1. Create global MCP configuration in ~/.claude/mcp_config.json
2. Navigate to directory A and run claude mcp list - servers appear
3. Navigate to directory B and run claude mcp list - servers do not appear
4. Verify global config file has not changed and is readable

Impact

This prevents consistent use of MCP tools across different projects, requiring workarounds or manual configuration per project.

What Should Happen?

mcps should be available no mater which directory I start claude in

Error Messages/Logs

### Working Directory: `/Users/rickmeier1/sb/fs-ci`

$ claude mcp list
Checking MCP server health...

atlassian: https://mcp.atlassian.com/v1/mcp (HTTP) - ✓ Connected
github: npx -y @modelcontextprotocol/server-github - ✓ Connected

✅ **Result:** Both MCP servers detected and connected successfully

### Working Directory: `/Users/rickmeier1/sb/mobile/mobile-ios`

$ claude mcp list
No MCP servers configured. Use `claude mcp add` to add a server.

❌ **Result:** No MCP servers detected, despite using the same global config

Steps to Reproduce

cd dir1
claude mcp add ...
claude mcp list
... in the list
cd ../dir2
claude mcp list
<no mcps>

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.7

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other

Additional Information

_No response_