deniedMcpServers setting does not block cloud (claude.ai) MCP servers

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?

Cloud-connected MCP servers (connected via Claude.ai account integrations) are not blocked by the deniedMcpServers setting in ~/.claude/settings.json. The tools still load and consume ~48,744 tokens of context window.

Steps to reproduce

1. Connect MCP integrations (ClickUp, Google Calendar, Slack, Fireflies, Gmail, Context7) via Claude.ai account
2. Add all of them to deniedMcpServers in ~/.claude/settings.json
3. Restart Claude Code
4. Run claude doctor

Expected behavior

Cloud MCP servers listed in deniedMcpServers should not load.

Actual behavior

claude doctor still reports all 6 servers loading ~48,744 tokens:

• claude_ai_ClickUp: 51 tools (~21,434 tokens)
• claude_ai_Google_Calendar: 9 tools (~12,720 tokens)
• claude_ai_Slack: 13 tools (~7,619 tokens)
• claude_ai_Fireflies: 14 tools (~3,083 tokens)
• claude_ai_Gmail: 7 tools (~2,674 tokens)

Tools are visible as deferred tools in the session context, confirming they are not blocked.

Use case

I want these integrations available in Claude Cowork but disabled in Claude Code to save context window.

Environment

• Claude Code: 2.1.81 (native)
• macOS 15.6.1

What Should Happen?

Cloud MCP servers listed in deniedMcpServers should not load their tools into the context window.

Error Messages/Logs

Steps to Reproduce

1. Connect MCP integrations (ClickUp, Google Calendar, Slack, Fireflies, Gmail, Context7) via Claude.ai account
2. Add all of them to deniedMcpServers in ~/.claude/settings.json
3. Restart Claude Code
4. Run claude doctor

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.81 (native)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_