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>
**Context:**
PR #163 fixed critical venv detection bugs but used aggressive
--break-system-packages flag as immediate fallback.
**Improvement:**
Now when no venv is found, the script:
1. Warns user about missing virtual environment
2. Offers to create one automatically (y/n prompt)
3. If yes: Creates venv, activates it, proceeds safely
4. If creation fails: Falls back to system install with warning
5. If no: Proceeds with system install but shows clear warning
**Benefits:**
- Encourages best practices (venv usage)
- Less aggressive about bypassing system protections
- Still supports system install when needed
- Better user experience with clear choices
**Backward Compatibility:**
- All three original scenarios still work
- Only adds new prompt in "no venv" scenario
- Default behavior unchanged for existing venv users
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
## ✅ Merged - All Bugs Fixed
Excellent work fixing both critical bugs from the initial review! All 390 tests passing.
**Original bugs fixed:**
- ✅ Double "install" command issue resolved
- ✅ pytest line now uses $PIP_INSTALL_CMD
**What's merged:**
- Virtual environment detection (active venv)
- Auto-activation of inactive venv/
- System install fallback with --user --break-system-packages
**Next:** Will add refinements to the system install fallback in a follow-up commit.
🤖 Merged with [Claude Code](https://claude.com/claude-code)
