[BUG] Allow disabling managed integrations (connectors) per product (Claude Code vs Cowork)

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?

Description

Managed integrations connected via claude.ai/settings/connectors (e.g. Slack, Gmail, Google Calendar) are injected into all Claude products that share the account. There is no way to enable an integration for one product (e.g. Cowork) while disabling it for another (e.g. Claude Code).

Problem

In Claude Code, managed integration tools (e.g. mcp__claude_ai_Slack__*) are loaded into the context window even when they are irrelevant to the coding session. This:

• Wastes context window tokens on tool definitions that will never be used.
• Adds noise to the tool list, increasing the chance of unintended tool selection.
• Cannot be prevented with permissions.deny or --disallowed-tools, as those block execution but still load the definitions into the prompt.

What Should Happen?

Current Workarounds Identified

• Disconnecting the integration account-wide at claude.ai/settings/connectors (removes it from Cowork too).
• Launching every session with --strict-mcp-config (tedious, disables all non-explicit MCP servers).

Proposed solution

Allow users to disable specific managed integrations for Claude Code. Possible approaches:

• A setting in ~/.claude/settings.json, e.g. "disabledManagedIntegrations": ["slack"], that prevents the tool definitions from being loaded into the context at all.
• Per-product toggles on the claude.ai/settings/connectors page.
• A claude mcp disable-managed <name> CLI command.

The key requirement is that disabled integrations must not be loaded into the context window, not merely blocked from execution.

Error Messages/Logs

I would never use MCP tools in my project, let alone have Claude Code call Slack, but here I am wasting 5% of all sessions' context window with these MCP tool definitions:

Context Usage      
     ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛀ ⛁ ⛀   claude-opus-4-6 · 143k/200k tokens (71%)                                                                       
     ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁                                                                                                                
     ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁   Estimated usage by category                                                                                    
     ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁   ⛁ System prompt: 3.6k tokens (1.8%)                                                                            
     ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁   ⛁ System tools: 9.8k tokens (4.9%)                                                                             
     ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁   ⛁ Custom agents: 612 tokens (0.3%)
     ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁ ⛁   ⛁ Memory files: 2.4k tokens (1.2%)                                                                             
     ⛁ ⛁ ⛁ ⛶ ⛶ ⛶ ⛶ ⛶ ⛶ ⛶   ⛁ Skills: 498 tokens (0.2%)
     ⛶ ⛶ ⛶ ⛝ ⛝ ⛝ ⛝ ⛝ ⛝ ⛝   ⛁ Messages: 126.9k tokens (63.4%)
     ⛝ ⛝ ⛝ ⛝ ⛝ ⛝ ⛝ ⛝ ⛝ ⛝   ⛶ Free space: 23k (11.6%)
                           ⛝ Autocompact buffer: 33k tokens (16.5%)

     MCP tools · /mcp (loaded on-demand)

     Available
     └ mcp__claude_ai_Slack__slack_send_message
     └ mcp__claude_ai_Slack__slack_schedule_message
     └ mcp__claude_ai_Slack__slack_create_canvas
     └ mcp__claude_ai_Slack__slack_search_public
     └ mcp__claude_ai_Slack__slack_search_public_and_private
     └ mcp__claude_ai_Slack__slack_search_channels
     └ mcp__claude_ai_Slack__slack_search_users
     └ mcp__claude_ai_Slack__slack_read_channel
     └ mcp__claude_ai_Slack__slack_read_thread
     └ mcp__claude_ai_Slack__slack_read_canvas
     └ mcp__claude_ai_Slack__slack_read_user_profile
     └ mcp__claude_ai_Slack__slack_send_message_draft

Steps to Reproduce

1. Enable Slack integration from Claude Cowork on Windows 11 desktop app.
2. Go to terminal on WSL2.
3. Start a Claude Code session.
4. Run /context to see the Slack MCP tools enabled from the Slack integration in Claude Cowork.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.56

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_