MCP Tools Not Available to AI Despite Connected Status

MCP Tools Not Available to AI Despite "✓ Connected" Status

Summary

MCP servers show "✓ Connected" status in claude mcp list and server processes are verified running, but their tools are not available to the AI in Claude Code sessions.

Environment

• Claude Code Version: 0.2.39 (CLI)
• Platform: WSL2 (Ubuntu on Windows)
• OS: Linux 6.6.87.2-microsoft-standard-WSL2
• Date: 2025-09-29

Steps to Reproduce

1. Configure MCP server in ~/.claude/claude_desktop_config.json:

{
  "mcpServers": {
    "caelum-knowledge-management": {
      "command": "node",
      "args": ["/mnt/c/ss/caelum/knowledge-management-server/build/index.js"],
      "env": {
        "CAELUM_ENV_FILE": "/home/rford/.caelum/.env",
        "QDRANT_URL": "http://10.32.3.27:6333"
      },
      "timeout": 30000,
      "description": "Knowledge management with semantic search and documentation storage"
    }
  }
}

1. Verify server is running:

$ claude mcp list
caelum-knowledge-management: node /mnt/c/ss/caelum/knowledge-management-server/build/index.js - ✓ Connected

$ ps aux | grep knowledge-management
rford    88151  0.0  0.5 1094524 89212 ?       Sl   08:15   0:00 node /mnt/c/ss/caelum/knowledge-management-server/build/index.js

1. Verify tools are defined in server code (build/index.js lines 93-129):

this.server.setRequestHandler(ListToolsRequestSchema, async () => ({
    tools: [
        {
            name: 'create_document',
            description: 'Create a new document in the knowledge base',
            inputSchema: CreateDocumentSchema,
        },
        {
            name: 'search_documents',
            description: 'Search documents in the knowledge base',
            inputSchema: SearchDocumentsSchema,
        },
        // ... 4 more tools defined
    ]
}));

1. Start new Claude Code terminal session
2. Attempt to use tool in AI session:

mcp__caelum-knowledge-management__create_document(...)

Expected Behavior

Tools should be available as:

• mcp__caelum-knowledge-management__create_document
• mcp__caelum-knowledge-management__search_documents
• mcp__caelum-knowledge-management__get_document
• mcp__caelum-knowledge-management__update_document
• mcp__caelum-knowledge-management__delete_document
• mcp__caelum-knowledge-management__list_documents

Actual Behavior

Error: No such tool available: mcp__caelum-knowledge-management__create_document

Additional Context

Session Start Hook Shows Tools Available

The session start hook message displays:

🚀 [CAELUM MCP] AI-Powered Development Tools Available:
  📊 Business Intel: research_market
  🔍 Code Analysis: analyze_code
  🔄 Workflows: create_workflow, execute_workflow
  🎯 Opportunities: discover_opportunities
  📱 Multi-device: Device orchestration
  📧 Notifications: Cross-platform alerts
Type /mcp to see all available tools!

However, these tools are also not actually callable by the AI.

Multiple Restarts Attempted

• Completely closed and reopened Claude Code terminal multiple times
• Verified server reconnects each time
• Issue persists across all restarts

Other MCP Servers Affected

The same issue affects multiple MCP servers:

• caelum-ollama-pool: ✓ Connected (tools not available)
• caelum-device-orchestration: ✓ Connected (tools not available)
• caelum-project-intelligence: ✓ Connected (tools not available)
• caelum-notifications: ✓ Connected (tools not available)
• caelum-development-session: ✓ Connected (tools not available)
• caelum-opportunity-discovery: ✓ Connected (tools not available)
• caelum-business-intelligence: ✓ Connected (tools not available)
• sequential-thinking: ✓ Connected (tools not available)

Server Logs Show Successful Initialization

Server logs in ~/.caelum/logs/kms-combined.log show:

{"level":"info","message":"Qdrant collection already exists","collection":"caelum_knowledge","timestamp":"2025-09-29T..."}
{"level":"info","message":"Qdrant vector database initialized successfully","url":"http://10.32.3.27:6333","timestamp":"2025-09-29T..."}
{"level":"info","message":"Caelum Knowledge Management Server running on stdio (with Qdrant vector database)","timestamp":"2025-09-29T..."}

Impact

• Cannot use MCP tools for knowledge storage
• Cannot leverage custom MCP servers despite successful connection
• Blocks workflow automation and knowledge management functionality

Workaround

Store data in local markdown files until issue is resolved.

Related Issues

• #467 - MCP tool calls not working in Claude Code
• #3426 - Claude Code fails to expose MCP tools to AI sessions
• #1611 - MCP servers fail to connect despite correct configuration

Diagnosis

The issue appears to be that Claude Code successfully:

1. Starts MCP server processes
2. Establishes connection to servers
3. Reports "✓ Connected" status

But fails to:

1. Query the server's tool list
2. Expose those tools to the AI session
3. Allow the AI to invoke the tools

This suggests a disconnect between the MCP server connection layer and the AI context/tool availability layer.