MCP server tools not loaded into AI function set despite showing as connected (v2.0.54 macOS)

Description

MCP server tools are not being loaded into Claude AI's function set in Claude Code v2.x, despite the MCP server showing as "connected" in the UI and working correctly.

Environment

• Claude Code Version: v2.0.54
• OS: macOS (Darwin 25.1.0)
• MCP Server: serena (but likely affects all MCP servers with similar architecture)

Problem

When an MCP server (serena) is configured and starts successfully:

1. ✅ MCP server starts without errors
2. ✅ Shows as "connected" in /mcp UI
3. ✅ Server logs show tools are registered
4. ❌ Tools don't appear in /context output
5. ❌ Tools not available in Claude AI's function set
6. ❌ ListMcpResourcesTool returns empty array for the server

Other MCP servers (atlassian, pagerduty, context7) work correctly, suggesting this is specific to certain types of MCP servers.

Configuration

{
  "type": "stdio",
  "command": "uvx",
  "args": [
    "--from",
    "git+https://github.com/oraios/serena",
    "serena",
    "start-mcp-server",
    "--context",
    "ide-assistant",
    "--project",
    "/path/to/project"
  ],
  "env": {}
}

Evidence

MCP Server logs (serena working correctly):

INFO Starting MCP server with 23 tools: ['list_dir', 'find_file', 'search_for_pattern', 
'get_symbols_overview', 'find_symbol', 'find_referencing_symbols', ...]
INFO MCP server lifetime setup complete

Claude AI's perspective:

• "I don't see the serena MCP tools available in my current environment"
• /context doesn't show serena tools
• ListMcpResourcesTool with server=serena returns []

UI shows:

• Serena appears as "connected" in /mcp menu
• No error messages or warnings

Steps to Reproduce

1. Configure serena MCP server in ~/.claude.json
2. Start Claude Code - serena shows as "connected"
3. Start a conversation and check /context
4. Ask AI to list MCP resources: ListMcpResourcesTool
5. Serena tools are missing despite connection

Expected Behavior

When an MCP server shows as "connected", its tools should be:

• Available in the AI's function set
• Visible in /context output
• Callable by the AI when requested

Additional Notes

• This persists across multiple restarts and new sessions
• Tested with and without various configuration flags
• Serena maintainer couldn't reproduce on Windows (version not specified)
• Issue seems specific to Claude Code v2.x (possibly macOS-specific?)
• Related upstream issue: https://github.com/oraios/serena/issues/780

Impact

This makes certain MCP servers unusable in Claude Code v2.x on macOS, despite them working correctly at the protocol level.