[BUG] Persistent MCP server diagnostic alert after removing configuration

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?

Bug Report: Persistent MCP Server Alert for Removed Configuration

Description

The Claude Code diagnostics (/doctor) shows a persistent "1 setup issue: MCP" alert for the plane MCP server, even after completely removing it from all configuration files. The alert only appears when Claude Code is launched from a specific project directory (~/Documents/Claude), but not when launched from the root home directory.

Environment

• Claude Code Version: 2.1.165
• Platform: macOS (darwin-arm64)
• OS Version: Darwin 25.5.0
• Environment: VSCode Extension
• Model: Sonnet 4.5

Key Observations

1. Location-specific: Alert appears when Claude Code is launched from ~/Documents/Claude but NOT when launched from root home directory (~)
2. Configuration verified clean: Extensive search confirmed no plane references in any .json files
3. Restart ineffective: Full quit/restart of Claude Code and VSCode does not clear the alert
4. Daemon restart unavailable: claude daemon restart command is disabled in this version

Investigation Performed

Searched for plane references in:

• All ~/.claude/**/*.json files
• All ~/Documents/Claude/.claude/**/*.json files
• Project session files in ~/.claude/projects/-Users-abram-goglanian-Documents-Claude/
• VSCode extension directory
• Running processes (no orphaned plane MCP processes found)

Hypothesis

The VSCode extension may be caching project-specific MCP server state that persists across restarts, independent of the actual configuration files. This cached state is not being invalidated when MCP server configurations are removed.

Workaround Attempted

• Setting "plane": { "disabled": true } in mcp.json (did not resolve)
• Completely removing plane from mcp.json (did not resolve)
• Full restart of Claude Code and VSCode (did not resolve)
• Clearing VSCode extension cache (no cache directory found)

Additional Context

Original plane configuration was added via:

claude mcp add-json plane '{
  "type": "http",
  "url": "https://mcp.plane.so/http/api-key/mcp",
  "headers": {
    "Authorization": "plane_api_70b04d5ece3b4723b131628e8fecefe9",
    "X-Workspace-slug": "plane.int.vastspace.com/vast"
  }
}'

Later changed to OAuth transport via npx mcp-remote@latest https://mcp.plane.so/http/mcp

Requested Fix

1. Clear any cached MCP server state when configuration files are modified
2. Provide a way to force-refresh MCP server discovery/diagnostics
3. Or provide claude daemon restart capability to fully reset state
4. Document where project-specific MCP state is cached so users can manually clear it

Impact

While this appears to be a cosmetic issue (the plane server doesn't actually load since it's not in config files), the persistent diagnostic alert is misleading and cannot be cleared through normal means.

What Should Happen?

Expected Behavior

No MCP setup alerts should appear, since the plane MCP server has been completely removed from all configuration files.

Actual Behavior

Diagnostics shows:

⚠ 1 setup issue: MCP · /doctor

When running /doctor, it indicates the plane server still needs authentication or has configuration issues.

Error Messages/Logs

Steps to Reproduce

Steps to Reproduce

1. Previously had plane MCP server configured in ~/.claude/mcp.json (configured via claude mcp add-json command on June 4, 2026)
2. Removed plane configuration by setting ~/.claude/mcp.json to:

``json
{
"mcpServers": {}
}
``

1. Verified no plane references in:

• ~/.claude/mcp.json ✓ Empty
• ~/.claude/mcp-needs-auth-cache.json ✓ Empty
• ~/Documents/Claude/.claude/settings.json ✓ Only contains standards MCP server
• ~/Documents/Claude/.claude/mcp.json ✓ Only contains vast-standards server
• ~/Documents/Claude/.claude/settings.local.json ✓ Only permissions config

1. Quit and restarted Claude Code completely (Cmd+Q, relaunch)
2. Launched Claude Code from ~/Documents/Claude directory
3. Run /doctor or view diagnostics

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.165

Platform

Google Vertex AI

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_