MCP Server stdout pollution prevents JSON-RPC communication

[spinbased]

Issue Description

The ruv-swarm MCP server outputs logging messages on stdout, which prevents proper JSON-RPC communication with MCP clients.

Problem

When running npx ruv-swarm mcp start, the server outputs various logs to stdout:

[ERROR] Failed to initialize pooled persistence {...}
[ca426a4e...] [INFO] ruv-swarm MCP server starting in stdio mode
[ca426a4e...] [INFO] Connection established {...}
🧠 Initializing ruv-swarm with WASM capabilities...
✅ WASM bindings loaded successfully
📊 Features: {...}

MCP Protocol Requirements:

• stdin/stdout must be dedicated to JSON-RPC messages
• All logging should go to stderr or log files
• stdout pollution breaks message parsing

Impact

MCP clients (like ABRAXAS v4.0) timeout after 10 seconds trying to parse tools/list responses because:

1. Send JSON-RPC request to stdin: {"jsonrpc":"2.0","id":1,"method":"tools/list","params":{}}
2. Expected response on stdout: {"jsonrpc":"2.0","id":1,"result":{...}}
3. Actual response: Mixed with log messages, unparseable

Expected Behavior

// stdout: ONLY JSON-RPC messages
{"jsonrpc":"2.0","id":1,"result":{"tools":[...]}}

// stderr: ALL logging
[INFO] ruv-swarm MCP server starting...
✅ WASM bindings loaded successfully

Reproduction Steps

# Terminal 1: Start MCP server
npx ruv-swarm mcp start

# Terminal 2: Send JSON-RPC message
echo '{"jsonrpc":"2.0","id":1,"method":"tools/list","params":{}}' | nc localhost 3000

# Result: Timeout or mixed output

Suggested Fix

Option 1: Separate Channels

// Route all logging to stderr
console.error('[INFO] Server starting...');  // Not console.log()

// Keep stdout clean for JSON-RPC
process.stdout.write(JSON.stringify(response) + '\n');

Option 2: Quiet Mode

npx ruv-swarm mcp start --quiet  # No logs on stdout
npx ruv-swarm mcp start --log-file=/tmp/ruv-swarm.log

Option 3: Configuration

{
  "mcp": {
    "protocol": "stdio",
    "logging": {
      "channel": "stderr",
      "level": "error"
    }
  }
}

Environment

• ruv-swarm version: 1.0.20
• Node.js: v22.18.0
• Platform: Windows 11 / Linux
• Used in: ABRAXAS v4.0 MCP integration

Related

This affects all MCP client integrations, including:

• Claude Code
• Claude Desktop
• ABRAXAS
• Any custom MCP clients

References

• MCP Specification
• MCP stdio Transport

Workaround

Until fixed, users can interact via CLI instead of MCP:

# Instead of MCP auto-connect
npx ruv-swarm init hierarchical 8
npx ruv-swarm orchestrate "task description"

Priority

High - Blocks MCP integration for all clients expecting clean stdio protocol.