[BUG] Mac app: Plugin MCP tools not available to the model despite showing "connected"

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?

Plugin MCP servers (e.g. plugin:product-management:atlassian) show as "✔ connected" in /mcp but their tools are never made available to the model in the Mac app. The same plugin works correctly in the CLI.

What Should Happen?

Expected: Plugin tools should be callable once the plugin shows as connected.

Actual: The plugin connection is established but tool definitions are not injected into the model's tool list. The model only sees built-in tools and non-plugin MCPs (e.g. mcp-registry, Claude_Preview).

Workaround: Use the CLI (claude command) — plugin tools load and work correctly there.

Error Messages/Logs

Steps to Reproduce

Steps to reproduce:

• Open Claude Code Mac app
• Run /mcp — confirm plugin:product-management:atlassian shows "✔ connected"
• Ask Claude to use an Atlassian/Jira tool (e.g. create an issue)
• Claude cannot find any Atlassian tools in its available tool list

Claude Model

Not sure / Multiple models

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.86

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_