Phantom Servers Persisting in MCP Status After Removal

Bug Description

Title: "MCP status command shows phantom servers after removal"

Description:
## Bug Description
The /mcp command shows persistent failed servers that don't exist in any MCP configuration.

## Steps to Reproduce

1. Configure MCP servers with claude mcp add
2. Remove all servers with claude mcp remove
3. Verify with claude mcp list (shows "No MCP servers configured")
4. Run /mcp command

## Expected Behavior
/mcp should show no servers or indicate no servers are configured

## Actual Behavior
/mcp shows 8 phantom failed servers: analytics, customer, database, department, filesystem,
llm, payment, registry

## Environment

• Platform: macOS (Darwin 24.5.0)
• Claude CLI version: 1.0.6 (Claude Code)
• These phantom servers persist after:
• claude mcp remove (all servers)
• Cache clearing (rm -rf ~/Library/Caches/claude-cli-nodejs)
• claude mcp reset-project-choices

## Evidence

• claude mcp list → "No MCP servers configured" ✓
• /mcp → Shows 8 failed servers ✗
• No .mcp.json file exists
• Servers not in Claude Desktop config

This makes MCP status unreliable and prevents proper MCP troubleshooting.

This clearly documents the inconsistency between the CLI commands and the interactive /mcp
status, which is definitely a bug that needs fixing.

Environment Info

• Platform: macos
• Terminal: vscode
• Version: 1.0.6
• Feedback ID: 233baee9-4e54-4a79-a16c-e1d830723946

Errors

[{"error":"Error: Command failed: security find-generic-password -a $USER -w -s \"Claude Code\"\nsecurity: SecKeychainSearchCopyNext: The specified item could not be found in the keychain.\n\n    at genericNodeError (node:internal/errors:983:15)\n    at wrappedFn (node:internal/errors:537:14)\n    at checkExecSyncError (node:child_process:888:11)\n    at execSync (node:child_process:960:15)\n    at tG (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:644:3921)\n    at file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:572:6758\n    at Q (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:532:16886)\n    at oR1 (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:572:5777)\n    at GG (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:572:5406)\n    at PU2 (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:1976:21167)","timestamp":"2025-05-31T21:46:31.343Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at Module.readSync (node:fs:740:18)\n    at Object.readSync (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:901)\n    at QG (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:545:260)\n    at BI (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:547:357)\n    at file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:1827:1455\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2025-05-31T21:47:49.728Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at Module.readFileSync (node:fs:441:20)\n    at Object.readFileSync (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:542:728)\n    at BI (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:547:375)\n    at file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:1827:1455\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2025-05-31T21:47:49.729Z"},{"error":"Error: Language not supported while highlighting code, falling back to markdown: \n    at file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:1368:418\n    at Object.useMemo (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:148:26271)\n    at cQ9.useMemo (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:52:15576)\n    at PC (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:1368:312)\n    at nw (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:148:19798)\n    at kO (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:150:42555)\n    at jO (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:150:38104)\n    at R$ (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:150:38032)\n    at XE (file:///Users/cosburn/.npm-global/lib/node_modules/@anthropic-ai/claude-code/cli.js:150:37886)\n    at $W (file:///Users/cosburn/.npm-g

Note: Error logs were truncated.