This PR improves MCP server configuration by updating all documentation to use the current server_fastmcp module and ensuring setup scripts automatically use virtual environment Python instead of system Python. ## Changes ### 1. Documentation Updates (server → server_fastmcp) Updated all references from deprecated `server` module to `server_fastmcp`: **User-facing documentation:** - examples/http_transport_examples.sh: All 13 command examples - README.md: Configuration examples and troubleshooting commands - docs/guides/MCP_SETUP.md: Enhanced migration guide with stdio/HTTP examples - docs/guides/TESTING_GUIDE.md: Test import statements - docs/guides/MULTI_AGENT_SETUP.md: Updated examples - docs/guides/SETUP_QUICK_REFERENCE.md: Updated paths - CLAUDE.md: CLI command examples **MCP module:** - src/skill_seekers/mcp/README.md: Updated config examples - src/skill_seekers/mcp/agent_detector.py: Use server_fastmcp module Note: Historical release notes (CHANGELOG.md) preserved unchanged. ### 2. Venv Python Configuration **setup_mcp.sh improvements:** - Added automatic venv detection (checks .venv, venv, and $VIRTUAL_ENV) - Sets PYTHON_CMD to venv Python path when available - **CRITICAL FIX**: Now updates PYTHON_CMD after creating/activating venv - Generates MCP configs with full venv Python path - Falls back to system python3 if no venv found - Displays detected Python version and path **Config examples updated:** - .claude/mcp_config.example.json: Use venv Python path - example-mcp-config.json: Use venv Python path - Added "type": "stdio" for clarity - Updated to use server_fastmcp module ### 3. Bug Fix: PYTHON_CMD Not Updated After Venv Creation Previously, when setup_mcp.sh created or activated a venv, it failed to update PYTHON_CMD, causing generated configs to still use system python3. **Fixed cases:** - When $VIRTUAL_ENV is already set → Update PYTHON_CMD to venv Python - When existing venv is activated → Set PYTHON_CMD="$REPO_PATH/venv/bin/python3" - When new venv is created → Set PYTHON_CMD="$REPO_PATH/venv/bin/python3" ## Benefits ### For Users: ✅ No deprecation warnings - All docs show current module ✅ Proper Python environment - MCP uses venv with all dependencies ✅ No system Python issues - Avoids "module not found" errors ✅ No global installation needed - No --break-system-packages required ✅ Automatic detection - setup_mcp.sh finds venv automatically ✅ Clean isolation - Projects don't interfere with system Python ### For Maintainers: ✅ Prepared for v3.0.0 - Documentation ready for server.py removal ✅ Reduced support burden - Fewer MCP configuration issues ✅ Consistent examples - All docs use same module/pattern ## Testing **Verified:** - ✅ All command examples use server_fastmcp - ✅ No deprecated module references in user-facing docs (0 results) - ✅ New module correctly referenced (129 instances) - ✅ setup_mcp.sh detects venv and generates correct config - ✅ PYTHON_CMD properly updated after venv creation - ✅ MCP server starts correctly with venv Python **Files changed:** 12 files (+262/-107 lines) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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Setup Quick Reference Card
One-Command Setup
./setup_mcp.sh
What Gets Configured
| Agent | Transport | Auto-Detected | Config Path (macOS) |
|---|---|---|---|
| Claude Code | stdio | ✅ | ~/.claude.json |
| Cursor | HTTP | ✅ | ~/Library/Application Support/Cursor/mcp_settings.json |
| Windsurf | HTTP | ✅ | ~/Library/Application Support/Windsurf/mcp_config.json |
| VS Code + Cline | stdio | ✅ | ~/Library/Application Support/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json |
| IntelliJ IDEA | HTTP | ✅ | ~/Library/Application Support/JetBrains/IntelliJIdea2024.3/mcp.xml |
Setup Steps
- ✅ Check Python (3.10+ recommended)
- ✅ Verify repo path
- ✅ Install dependencies (with venv option)
- ✅ Test transports (stdio + HTTP)
- ✅ Detect agents (automatic!)
- ✅ Configure agents (with merging)
- ✅ Start HTTP server (if needed)
- ✅ Test configs (validate JSON)
- ✅ Show instructions (next steps)
Common Workflows
Configure All Detected Agents
./setup_mcp.sh
# Choose option 1 when prompted
Select Individual Agents
./setup_mcp.sh
# Choose option 2 when prompted
# Answer y/n for each agent
Manual Configuration Only
./setup_mcp.sh
# Choose option 3 when prompted
# Copy manual config from output
HTTP Server Management
Start Server
# During setup
./setup_mcp.sh
# Choose option 1 for HTTP server
# Manual start
python3 -m skill_seekers.mcp.server_fastmcp --http --port 3000
Test Server
curl http://localhost:3000/health
Stop Server
# If you know PID
kill 12345
# Find and kill
pkill -f "skill_seekers.mcp.server_fastmcp"
View Logs
tail -f /tmp/skill-seekers-mcp.log
Configuration Files
Stdio Config (Claude Code, VS Code)
{
"mcpServers": {
"skill-seeker": {
"command": "python",
"args": ["-m", "skill_seekers.mcp.server_fastmcp"]
}
}
}
HTTP Config (Cursor, Windsurf)
{
"mcpServers": {
"skill-seeker": {
"url": "http://localhost:3000/sse"
}
}
}
Testing
Test Agent Detection
python3 -c "
import sys
sys.path.insert(0, 'src')
from skill_seekers.mcp.agent_detector import AgentDetector
for agent in AgentDetector().detect_agents():
print(f\"{agent['name']} ({agent['transport']})\")
"
Test Config Generation
python3 -c "
import sys
sys.path.insert(0, 'src')
from skill_seekers.mcp.agent_detector import generate_config
print(generate_config('claude-code', 'skill-seekers mcp'))
"
Test HTTP Server
# Start server
python3 -m skill_seekers.mcp.server_fastmcp --http --port 3000 &
# Test health
curl http://localhost:3000/health
# Stop server
pkill -f skill_seekers.mcp.server_fastmcp
Test in Agent
After restart, try these commands:
List all available configs
Generate config for React at https://react.dev
Estimate pages for configs/godot.json
Troubleshooting
Agent Not Detected
# Check if config directory exists
ls ~/Library/Application\ Support/Claude/ # macOS
ls ~/.config/claude-code/ # Linux
Config Merge Failed
# Check backup
cat ~/.config/claude-code/mcp.json.backup.*
# Validate JSON
jq empty ~/.config/claude-code/mcp.json
HTTP Server Won't Start
# Check port usage
lsof -i :3000
# Kill process
lsof -ti:3000 | xargs kill -9
# Use different port
python3 -m skill_seekers.mcp.server_fastmcp --http --port 8080
Agent Can't Connect
# Verify server running
curl http://localhost:3000/health
# Check logs
tail -f /tmp/skill-seekers-mcp.log
# Restart server
pkill -f skill_seekers.mcp.server_fastmcp
python3 -m skill_seekers.mcp.server_fastmcp --http --port 3000 &
Quick Commands
# Check Python version
python3 --version
# Test MCP server (stdio)
python3 -m skill_seekers.mcp.server_fastmcp
# Test MCP server (HTTP)
python3 -m skill_seekers.mcp.server_fastmcp --http --port 3000
# Check installed agents
python3 -c "import sys; sys.path.insert(0, 'src'); from skill_seekers.mcp.agent_detector import detect_agents; print(detect_agents())"
# Generate config for agent
python3 -c "import sys; sys.path.insert(0, 'src'); from skill_seekers.mcp.agent_detector import generate_config; print(generate_config('cursor', 'skill-seekers mcp', 3000))"
# Validate config JSON
jq empty ~/.config/claude-code/mcp.json
# Start HTTP server in background
nohup python3 -m skill_seekers.mcp.server_fastmcp --http --port 3000 > /tmp/skill-seekers-mcp.log 2>&1 &
# Health check
curl http://localhost:3000/health
# View logs
tail -f /tmp/skill-seekers-mcp.log
# Find server process
ps aux | grep skill_seekers.mcp.server_fastmcp
# Kill server
pkill -f skill_seekers.mcp.server_fastmcp
Environment Variables
# Virtual environment (if used)
source venv/bin/activate
# Check if in venv
echo $VIRTUAL_ENV
# Check Python path
which python3
File Locations
Setup Script
./setup_mcp.sh
Agent Detector Module
src/skill_seekers/mcp/agent_detector.py
MCP Server
src/skill_seekers/mcp/server_fastmcp.py
Documentation
docs/MULTI_AGENT_SETUP.md # Comprehensive guide
docs/SETUP_QUICK_REFERENCE.md # This file
docs/HTTP_TRANSPORT.md # HTTP transport guide
docs/MCP_SETUP.md # MCP integration guide
Config Paths (Linux)
~/.config/claude-code/mcp.json
~/.cursor/mcp_settings.json
~/.windsurf/mcp_config.json
~/.config/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
~/.config/JetBrains/IntelliJIdea2024.3/mcp.xml
Config Paths (macOS)
~/.claude.json
~/Library/Application Support/Cursor/mcp_settings.json
~/Library/Application Support/Windsurf/mcp_config.json
~/Library/Application Support/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
~/Library/Application Support/JetBrains/IntelliJIdea2024.3/mcp.xml
After Setup
- Restart agents (completely quit and reopen)
- Test commands in agent
- Verify HTTP server (if applicable)
- Read documentation for advanced features
Getting Help
- Documentation: docs/MULTI_AGENT_SETUP.md
- GitHub Issues: https://github.com/yusufkaraaslan/Skill_Seekers/issues
- MCP Docs: https://modelcontextprotocol.io/
Quick Validation Checklist
- Python 3.10+ installed
- Dependencies installed (
pip install -e .) - MCP server tests passed (stdio + HTTP)
- Agents detected
- Configs created/merged
- Backups created (if configs existed)
- HTTP server started (if needed)
- Health check passed (if HTTP)
- Agents restarted
- MCP tools working in agents
Version Info
Skill Seekers Version: 2.1.2+ Setup Script: Multi-agent auto-configuration Supported Agents: 5 (Claude Code, Cursor, Windsurf, VS Code + Cline, IntelliJ) Transport Types: stdio, HTTP Platforms: Linux, macOS, Windows