[BUG] Local stdio MCP server (sequential-thinking) still returns "disabled in connector settings" in Cowork mode despite working perfectly in Chat mode (macOS, Max plan) — #20377 not resolved

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?

The server-sequential-thinking MCP server is configured in claude_desktop_config.json and works flawlessly in regular Claude Chat mode. However, in Cowork mode, every call to the sequentialthinking tool returns:

"This tool has been disabled in your connector settings."

This occurs despite:

• The connector appearing in Settings > Connectors as "server-sequential-thinking"
• Tool permissions set to "Always allow"
• The MCP server starting and registering its tools successfully (confirmed via logs)
• The tool schema loading correctly into Cowork's tool registry

Steps to Reproduce:

1. Configure @modelcontextprotocol/server-sequential-thinking in claude_desktop_config.json
2. Restart Claude Desktop
3. Open a regular Chat conversation and use sequential thinking — works ✅
4. Open a Cowork conversation and use sequential thinking — "disabled in connector settings" ❌

Environment:

• macOS (Apple Silicon, MacBook Air)
• Claude Desktop v1.1.9493 (b58a0b) 2026-03-29 (NOT Claude Code CLI — filing here as this is Anthropic's shared issue tracker)
• Max plan
• MCP server: @modelcontextprotocol/server-sequential-thinking v2025.12.18

This is a reopening of #20377, which was closed but never resolved. Also reported in #23424, #27492, #24433, #31864, and #38783 — all pointing to the same unresolved problem over 2+ months.

What Should Happen?

Local stdio MCP servers configured in claude_desktop_config.json should be accessible in Cowork mode, the same as they are in Chat mode. The connector settings UI showing "Always allow" should be honored by the Cowork routing layer. The tool call should reach the MCP server instead of being intercepted by the PreToolUse hook.

Error Messages/Logs

Tool call response in Cowork mode:
"This tool has been disabled in your connector settings."

Server logs (consistent from Jan 29 - Mar 31, 2026):
- Server started and connected successfully
- MCP protocol handshake completed (protocolVersion 2025-11-25)
- sequentialthinking tool registered via tools/list response
- Server version: sequential-thinking-server v0.2.0
- No errors during initialization
- Server NEVER receives a tools/call request — the call is blocked at the Cowork routing layer before reaching the server

Steps to Reproduce

1. Add @modelcontextprotocol/server-sequential-thinking to claude_desktop_config.json:

   "server-sequential-thinking": {
     "command": "/opt/homebrew/opt/node@22/bin/npx",
     "args": ["-y", "@modelcontextprotocol/server-sequential-thinking"]
   }

1. Restart Claude Desktop
2. Open a regular Chat conversation → ask Claude to use sequential thinking → works ✅
3. Open a Cowork conversation → ask Claude to use sequential thinking → returns "This tool has been disabled in your connector settings" ❌

Note: The MCP server initializes successfully in both cases (confirmed via logs). The tool call is blocked at the Cowork routing layer (PreToolUse hook) before it ever reaches the MCP server.

Claude Model

None

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

Claude Desktop v1.1.9493 (b58a0b) 2026-03-29 (Not Claude Code CLI — using Claude Desktop Cowork mode)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Related issues (all reporting the same unresolved problem):

• #20377 — "Local / desktop MCP tools not exposed to claude cowork" (Closed, but NOT fixed)
• #23424 — "Local MCP Servers Still Not Working in Cowork Mode" (Closed as duplicate)
• #27492 — "Claude cowork MCP Issue continues"
• #24433 — "Always allow for MCP tools does not persist across Cowork sessions"
• #31864 — "Auto-update creates silent MCP extension conflict"
• #38783 — "Cowork browser automation tools missing after update"

Root cause: Cowork runs in a sandboxed VM that cannot reach local stdio-based MCP servers running on the host machine. Only HTTP-based connectors work. The PreToolUse hook blocks all local stdio tool calls with "disabled in connector settings" before they reach the MCP server.

This has persisted across multiple Claude Desktop versions over 2+ months (Jan–Mar 2026).