# CRITICAL FIX - Path and Tool Registration Issues
## Issue 1: Python Not Found (SOLVED)
**Error:** `spawn python ENOENT 2`
**Cause:** Claude Desktop can't find `python` command in its PATH
**Fix:** Use absolute path to Python executable
### ❌ OLD Config:
```json
{
"command": "python",
...
}
```
### ✅ NEW Config:
```json
{
"command": "/Users/cliffclarke/Claude_Code/codebase-mcp/.venv/bin/python",
...
}
```
---
## Issue 2: 0 Tools Returned (LIKELY FIXED)
**Symptom:** Server starts but `tools/list` returns empty array
**Possible causes:**
1. Async function not being called properly
2. Database session issues causing silent failures
3. Tool registration not working with MCP SDK version
**Fix:** Created `mcp_stdio_server_v2.py` with:
- Tools defined at module level (not in function)
- Simplified database session handling
- Better error logging
- Direct use of SessionLocal instead of get_db() generator
---
## Testing Instructions
### Step 1: Test minimal MCP server first
```bash
cd /Users/cliffclarke/Claude_Code/codebase-mcp
source .venv/bin/activate
# Test the minimal server (should show 1 tool)
echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"0.1.0","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}' | python test_minimal_mcp.py 2>&1
# Then test tools/list
echo '{"jsonrpc":"2.0","id":2,"method":"tools/list","params":{}}' | python test_minimal_mcp.py 2>&1
```
**Expected:** Should see "1 tools" in stderr debug output
### Step 2: Test v2 server
```bash
# Test the v2 server (should show 6 tools)
echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"0.1.0","capabilities":{},"clientInfo":{"name":"test","version":"1.0"}}}' | python -m src.mcp.mcp_stdio_server_v2 2>&1
echo '{"jsonrpc":"2.0","id":2,"method":"tools/list","params":{}}' | python -m src.mcp.mcp_stdio_server_v2 2>&1
```
**Expected:** Should see 6 tools listed
### Step 3: Update Claude Desktop config
Use `claude_desktop_config_FIXED.json`:
```json
{
"mcpServers": {
"codebase-mcp": {
"command": "/Users/cliffclarke/Claude_Code/codebase-mcp/.venv/bin/python",
"args": ["-m", "src.mcp.mcp_stdio_server_v2"],
"cwd": "/Users/cliffclarke/Claude_Code/codebase-mcp",
"env": {
"DATABASE_URL": "postgresql+asyncpg://cliffclarke@localhost:5432/codebase_mcp",
"OLLAMA_BASE_URL": "http://localhost:11434",
"OLLAMA_EMBEDDING_MODEL": "embeddinggemma:latest",
"LOG_LEVEL": "INFO",
"LOG_FILE": "/tmp/codebase-mcp.log"
}
}
}
}
```
**Key changes:**
1. ✅ `"command"`: Full path to Python
2. ✅ `"args"`: Changed to `src.mcp.mcp_stdio_server_v2`
### Step 4: Deploy
```bash
# Copy fixed config
cp claude_desktop_config_FIXED.json ~/Library/Application\ Support/Claude/claude_desktop_config.json
# Restart Claude Desktop
killall Claude
# Check logs
tail -f /tmp/codebase-mcp.log
```
---
## Debugging
### If still 0 tools:
```bash
# Check stderr output manually
python -m src.mcp.mcp_stdio_server_v2 2>&1 &
echo '{"jsonrpc":"2.0","id":2,"method":"tools/list","params":{}}' | python -m src.mcp.mcp_stdio_server_v2
# Should see tool list in response
```
### Check Claude Desktop logs:
```bash
# Find MCP logs
ls -la ~/Library/Logs/Claude/mcp*.log
# View latest
tail -100 ~/Library/Logs/Claude/mcp-server-codebase-mcp.log
```
### Check server logs:
```bash
tail -100 /tmp/codebase-mcp.log
```
---
## What Changed in v2
| Aspect | v1 | v2 |
|--------|----|----|
| Tools definition | Inside async function | Module level list |
| DB session | `async for db in get_db()` | Direct `SessionLocal()` |
| Error handling | Basic | Comprehensive with traceback |
| Logging | Minimal | Debug output included |
**Why module-level tools?** Ensures the tools list is always available and not dependent on any runtime state.
**Why direct SessionLocal?** The `get_db()` generator is designed for FastAPI dependency injection, not direct async iteration. Using SessionLocal directly gives us full control.
---
## Success Criteria
✅ **Minimal test server shows 1 tool**
✅ **V2 server shows 6 tools**
✅ **No ENOENT errors in Claude Desktop**
✅ **Server stays connected (no immediate disconnect)**
✅ **Tools visible in Claude Desktop hammer menu**
---
## If STILL Having Issues
Run the diagnostic script:
```bash
chmod +x diagnose.sh
./diagnose.sh > diagnostic_output.txt
```
This will collect:
- Claude Desktop config
- Claude Desktop logs
- Server logs
- Environment check
- Database/Ollama status
Share `diagnostic_output.txt` for further debugging.
---
**Confidence on path fix:** 100% - ENOENT is definitely a PATH issue
**Confidence on tools fix:** 85% - architectural fix, but need to test
**Next action:** Test minimal server first, then v2, then deploy to Desktop
