[BUG] Desktop (Code tab): desktop extension tools stay blocked — a legacy "server:tool" entry set to false cannot be cleared

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?

In the Code tab of the Claude Desktop app, every call to a tool of the "Affinity" desktop extension (Canva) is rejected by the app's PreToolUse check: "This tool has been disabled in your connector settings". All visible settings are correct, and the same extension works normally in the Chat tab.

Diagnosis:

• Each Code session's enabledMcpTools map lists all 11 tools twice: "local:Affinity:<tool>": true (written by the "+" menu → Connectors toggle) and "Affinity:<tool>": false (legacy format).
• The PreToolUse check builds the key <server>:<tool> from the tool name (mcp__Affinity__x → Affinity:x), so the legacy entry always wins.
• These Affinity:<tool> entries are also persisted in ~/Library/Application Support/Claude/mcp-user-tool-toggles.json and in every session created since the extension was installed (August 2026). No UI can clear them.

What Should Happen?

The tool should run (or ask for approval for a write tool), exactly as it does in the Chat tab.

Error Messages/Logs

PreToolUse:mcp__Affinity__list_sdk_documentation hook error: This tool has been disabled in your connector settings.

Steps to Reproduce

1. Install the "Affinity" desktop extension (Canva, 1.0.8) and enable its MCP server in Affinity 3.3 (port 6767 listening).
2. Customize → Affinity: extension enabled; read-only tools set to "Always allow", write tools set to "Needs approval".
3. In a Code tab session, "+" menu → Connectors: Affinity toggled on.
4. Ask Claude to call any Affinity tool, e.g. list_sdk_documentation.
5. The call is rejected with the error above. The same request in the Chat tab works.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.286 (bundled with Claude Desktop 2.19675.0)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other

Additional Information

Environment: Claude Desktop 2.19675.0 (Code tab, not a terminal), macOS 27.0, "Affinity" desktop extension 1.0.8, Affinity 3.3.0 (4850).

Already tried, no effect:

• Toggling Affinity off and on in the "+" menu → Connectors.
• Uninstalling and reinstalling the extension, with Claude restarted.
• Starting a new Code session.

Likely cause: key format mismatch between the toggle (local: prefix for desktop extensions) and the PreToolUse check. Legacy keys should be migrated or purged, or the check should read both formats.