[BUG] Official connectors (e.g., Supabase) not available as tools in agentic/code mode

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?

Official connectors installed through Claude Desktop's Connectors settings (Settings → Connectors) are not exposed as callable tools when Claude operates in agentic/code mode.

What Should Happen?

Install the official Supabase connector via Settings → Connectors
Authorize and connect to a Supabase project
Set tool permissions to "Always allow" for both read-only and write/delete tools
Restart Claude Desktop
In a conversation, ask Claude to use Supabase tools programmatically (e.g., list tables, query schema)
Expected behavior:

The 18 read-only tools and 11 write/delete tools shown in the connector's permissions should be available for Claude to call programmatically, similar to how custom MCP servers defined in claude_desktop_config.json expose their tools.

Actual behavior:

Claude cannot access any tools from the official connector. Tool calls like mcp__supabase__list_projects or variations return "No such tool available." The connector only works in Chat and Co-work modes, not in code/agentic mode.

Error Messages/Logs

Steps to Reproduce

Steps to reproduce:

Install the official Supabase connector via Settings → Connectors
Authorize and connect to a Supabase project
Set tool permissions to "Always allow" for both read-only and write/delete tools
Restart Claude Desktop
In a conversation, ask Claude to use Supabase tools programmatically (e.g., list tables, query schema)
Expected behavior:

The 18 read-only tools and 11 write/delete tools shown in the connector's permissions should be available for Claude to call programmatically, similar to how custom MCP servers defined in claude_desktop_config.json expose their tools.

Actual behavior:

Claude cannot access any tools from the official connector. Tool calls like mcp__supabase__list_projects or variations return "No such tool available." The connector only works in Chat and Co-work modes, not in code/agentic mode.

Claude Model

Not sure / Multiple models

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

Version 1.1.1890 (af393c)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Workaround:

Adding a custom MCP server entry to ~/Library/Application Support/Claude/claude_desktop_config.json works:

{
"mcpServers": {
"supabase": {
"command": "npx",
"args": ["-y", "@supabase/mcp-server-supabase", "--access-token", "TOKEN", "--project-ref", "PROJECT_REF"]
}
}
}

This exposes tools that Claude can call programmatically.

Impact:

Users cannot benefit from the simpler OAuth-based official connector setup when using Claude in agentic mode. They must manually configure MCP servers with access tokens, defeating the purpose of the official connector's streamlined authentication flow.

Environment:

Claude Desktop (macOS)
Official Supabase connector (https://mcp.supabase.com/mcp)