[BUG] Desktop Extensions (DXT) not available in Code tab despite connector toggle showing them

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?

Extensions installed via the Claude Desktop app (DXT format) are visible as toggleable connectors in the Code tab (via + → Connectors), but enabling the toggle does not make the extension's MCP tools available to the Code session.

Steps to reproduce:

1. Install a DXT extension via the Desktop app (e.g., Metabase MCP)
2. Configure it with credentials through the Desktop UI
3. Open the Code tab
4. Click + → Connectors → Enable the extension toggle
5. Try to use the extension's tools — they are not available

Investigation findings:

• Desktop Extensions are stored in ~/Library/Application Support/Claude/Claude Extensions/
• Extension credentials are stored encrypted in ~/Library/Application Support/Claude/Claude Extensions Settings/
• The Code tab's MCP engine only reads from ~/.claude/mcp_settings.json, which does not include Desktop-managed Extensions
• The same sync gap exists for Skills: the app stores them under ~/Library/Application Support/Claude/local-agent-mode-sessions/skills-plugin/, but the Code tab only reads ~/.claude/skills/

Workaround: Manually add the extension's MCP server to ~/.claude/mcp_settings.json with plaintext credentials. For skills, symlink the app's skill directories into ~/.claude/skills/.

What Should Happen?

Toggling a DXT extension ON in the Code tab's Connectors menu should inject the extension's MCP server config (including decrypted credentials) into the Code session, making its tools available — just like it works in Chat and Cowork modes.

Similarly, skills installed via the Desktop app should be automatically available in Code tab sessions without needing manual symlinks.

Error Messages/Logs

No error messages — the extension toggle silently does nothing. The MCP tools simply never appear in the Code session.

Steps to Reproduce

1. Install a DXT extension via Desktop app (e.g., Metabase MCP from ant.dir.gh.jerichosequitin.metabase)
2. Configure it with API credentials through the Desktop Extensions UI
3. Verify it works in Chat or Cowork mode
4. Switch to the Code tab
5. Click + → Connectors → toggle the extension ON
6. Ask Claude to use the extension's tools (e.g., "query Metabase")
7. Claude reports the tools are not available

The extension's MCP server is never started for the Code session. Only servers defined in ~/.claude/mcp_settings.json are loaded.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

Claude Desktop App (Code tab) - latest as of 2026-02-26

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other

Additional Information

This bug also affects Skills — skills installed via the Desktop app are stored in a different directory than what the Code tab reads. The same config sync issue applies to both DXT Extensions (MCPs) and Skills.

Using the Claude Desktop App Code tab on macOS. The DXT extension tested was Metabase MCP (ant.dir.gh.jerichosequitin.metabase v1.1.4).

Terminal/Shell is "Other" because this is the Desktop App's built-in Code tab, not a standalone terminal.