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MCP Connection Fix - Implementation Complete ✅

Summary

Successfully implemented the fix for MCP connection issues with Claude Code CLI. The problem was caused by using an incorrect entry point that didn't properly handle stdio transport for MCP connections.

Changes Made

1. Created Proper Stdio Entry Point ✅

  • File: src/mcp_server/stdio_full_mcp.py
  • Action: Copied from stdio_full_mcp.py.backup to make it a proper Python module
  • Purpose: Provides correct stdio transport implementation using FastMCP's run() method

2. Updated Documentation ✅

Updated three documentation files to reference the correct entry point:

  1. docs/CLAUDE_CLI_SETUP.md

    • Lines 43 & 60: Changed from src.mcp_server.mcp_app to src.mcp_server.stdio_full_mcp

  2. docs/FINALIZATION_SUMMARY.md

    • Line 51: Changed from src.mcp_server.mcp_app to src.mcp_server.stdio_full_mcp

  3. docs/MCP_SERVER_TESTING_GUIDE.md

    • Line 117: Changed from src.mcp_server.mcp_app to src.mcp_server.stdio_full_mcp
    • Added PYTHONPATH environment variable

3. Created Fix Documentation ✅

  • File: docs/MCP_CONNECTION_FIX.md
  • Purpose: Detailed explanation of the problem, solution, and migration guide

4. Verified Environment Configuration ✅

  • File: deployment/docker/.env
  • Status: Confirmed MCP_ENABLED=true is set correctly

What Changed in the Configuration

Before (Incorrect) ❌

{
  "context": {
    "command": "docker",
    "args": ["exec", "-i", "context-server", "python", "-m", "src.mcp_server.mcp_app"],
    "env": {
      "MCP_ENABLED": "true",
      "PYTHONPATH": "/app"
    }
  }
}

After (Correct) ✅

{
  "context": {
    "command": "docker",
    "args": ["exec", "-i", "context-server", "python", "-m", "src.mcp_server.stdio_full_mcp"],
    "env": {
      "MCP_ENABLED": "true",
      "PYTHONPATH": "/app"
    }
  }
}

Key Change: mcp_app → stdio_full_mcp

Testing Instructions

Step 1: Verify Docker Services are Running

cd deployment/docker
docker-compose ps

Expected output should show all services as "Up (healthy)":

  • context-server
  • postgres
  • redis
  • qdrant
  • ollama

If not running:

docker-compose up -d

Step 2: Update Claude CLI Configuration

Linux/Mac:

nano ~/.config/claude/mcp_servers.json

Windows:

notepad %APPDATA%\Claude\mcp_servers.json

Update the configuration to use stdio_full_mcp as shown above.

Step 3: Restart Claude Code CLI

  1. Close Claude Code CLI completely
  2. Wait 5 seconds
  3. Reopen Claude Code CLI

Step 4: Test the Connection

In Claude Code CLI, ask:

Can you check the health of the Context MCP server?

Expected Response: Claude should successfully call the health_check tool and return server status information including:

  • Server name: "Context"
  • Version: "0.1.0"
  • Status: "running"
  • Connection state: "connected"

Step 5: Test MCP Tools

Try these commands to verify MCP tools are working:

  1. List available tools:

    What MCP tools are available from the Context server?

  2. Test semantic search:

    Search for authentication functions in the codebase using the Context server.

  3. Check indexing status:

    What's the current indexing status of the Context server?

Troubleshooting

If Connection Still Fails

  1. Check Docker logs:

    docker logs context-server | tail -50

    Look for:

    • "Starting FULL STDIO MCP server (all tools)..."
    • "FastMCP server instance created successfully"
    • "Starting FastMCP stdio transport..."

  2. Verify the module exists:

    docker exec context-server ls -la /app/src/mcp_server/stdio_full_mcp.py

  3. Test the entry point directly:

    docker exec -i context-server python -m src.mcp_server.stdio_full_mcp

    Press Ctrl+C to exit after verifying it starts without errors.

  4. Check MCP_ENABLED setting:

    docker exec context-server env | grep MCP_ENABLED

    Should return: MCP_ENABLED=true

Common Issues

Issue: "ModuleNotFoundError: No module named 'src.mcp_server.stdio_full_mcp'" Solution: The file wasn't copied correctly. Run:

docker exec context-server ls -la /app/src/mcp_server/stdio_full_mcp.py

Issue: Claude CLI shows "Connection timeout" Solution:

  1. Restart Docker services: docker-compose restart context-server
  2. Check logs: docker logs context-server
  3. Verify Claude CLI config file syntax is valid JSON

Issue: "MCP server is disabled" Solution: Edit deployment/docker/.env and set MCP_ENABLED=true, then restart:

docker-compose restart context-server

Next Steps

After successful connection:

  1. ✅ Index your codebase
  2. ✅ Test semantic search functionality
  3. ✅ Try context-aware prompt enhancement
  4. ✅ Explore cross-language analysis tools

Files Modified

  • ✅ src/mcp_server/stdio_full_mcp.py (created from backup)
  • ✅ docs/CLAUDE_CLI_SETUP.md (updated entry point)
  • ✅ docs/FINALIZATION_SUMMARY.md (updated entry point)
  • ✅ docs/MCP_SERVER_TESTING_GUIDE.md (updated entry point)
  • ✅ docs/MCP_CONNECTION_FIX.md (new documentation)
  • ✅ MCP_FIX_IMPLEMENTATION_SUMMARY.md (this file)

References