MCP servers show as "connected" but tools not available to LLM in VSCode extension (Windows)

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

MCP servers successfully connect and show as "connected" in the /mcp UI, but the tools are not available to Claude in conversations. When attempting to use MCP tools, I get "Error: No such tool available" even though the server status shows connected with tools listed.

Steps to Reproduce

1. Configure MCP servers in ~/.claude.json under the project key C:/Users/****/Documents/Prosjekter/****
2. Configured servers:

• Supabase (HTTP): https://mcp.supabase.com/mcp?project_ref=kdzojuqivzawsklphosc
• Sentry (stdio): npx @sentry/mcp-server@latest with auth token
• Stripe (HTTP): https://mcp.stripe.com

1. Restart VSCode and Claude Code extension
2. Run /mcp command - shows servers as "connected" with tools count (e.g., "22 tools" for Sentry, "20 tools" for Supabase)
3. Ask Claude to use an MCP tool (e.g., "list all tables in Supabase")
4. Claude attempts to call the tool but gets "Error: No such tool available"

Expected Behavior

When MCP servers show as "connected" with tools available, Claude should be able to invoke those tools successfully.

Actual Behavior

• /mcp UI shows servers as "connected" ✅
• Tools count is displayed (e.g., "20 tools") ✅
• But when Claude tries to call mcp__supabase__list_tables or any other MCP tool, it errors: "Error: No such tool available" ❌
• The tools don't appear in Claude's available function list

Environment

• OS: Windows 11
• Claude Code version: 2.1.31 (latest)
• VSCode extension (not CLI)
• Shell: Git Bash
• Node.js: Available via npx
• Project path: C:/Users/****/Documents/Prosjekter/*****

Configuration

Path case sensitivity issue was previously resolved - only ONE project entry exists with uppercase C: in ~/.claude.json:

"projects": {
  "C:/Users/*****/Documents/Prosjekter/*****": {
    "mcpServers": {
      "sentry": { "type": "stdio", "command": "npx", "args": [...] },
      "supabase": { "type": "http", "url": "https://mcp.supabase.com/..." },
      "stripe": { "type": "http", "url": "https://mcp.stripe.com" }
    },
    "disabledMcpServers": []
  }
}


### What Should Happen?

When MCP servers are configured correctly and show as "connected" in the `/mcp` UI with tools listed, Claude should be able to invoke those tools in conversations. For example, calling `mcp__supabase__list_tables` should successfully query the Supabase database and return results.


### Error Messages/Logs

```shell
When attempting to use MCP tools, Claude returns:

Error: No such tool available: mcp__supabase__list_tables

Example tool calls attempted:
- mcp__supabase__list_tables
- mcp__supabase__execute_sql
- mcp__sentry__list_projects
- mcp__sentry__list_organizations

All return the same "No such tool available" error despite the `/mcp` UI showing:
- sentry: ✓ connected (22 tools)
- supabase: ✓ connected (20 tools)
- stripe: ✗ failed (authentication issue - separate from this bug)

Steps to Reproduce

1. On Windows, configure MCP servers in ~/.claude.json:

{
"projects": {
"C:/Users/[user]/Documents/Prosjekter/****": {
"mcpServers": {
"sentry": {
"type": "stdio",
"command": "npx",
"args": ["@sentry/mcp-server@latest", "--access-token=...", "--host=..."]
},
"supabase": {
"type": "http",
"url": "https://mcp.supabase.com/mcp?project_ref=..."
}
},
"disabledMcpServers": []
}
}
}

1. Restart VSCode completely
2. Open the project in VSCode with Claude Code extension
3. Run /mcp command
4. Observe: Servers show as "connected" with tool counts
5. Start a conversation and ask Claude to "list all tables in Supabase"
6. Observe: Claude attempts to call the tool but gets "Error: No such tool available"
7. Try in multiple new conversations - same result

Claude Model

None

Is this a regression?

I don't know

Last Working Version

It worked before, but unknown when it broke.

Claude Code Version

2.1.31

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

_No response_