Check the build is current:

cd ${CLAUDE_PLUGIN_ROOT}
npm run build

If build fails:

Check tsconfig.json for TypeScript errors
Run npm install to ensure dependencies are installed
Check Node.js version (requires 18+)

2. MCP Server Connectivity

Test that MCP servers can connect. In execute_code:

// Check which clients are available
console.log("Available:", Object.keys({ serena, gemini, context7 }));

// Test a simple call
try {
  const result = await serena.get_active_project({});
  console.log("Serena OK:", result ? "connected" : "no project");
} catch (e) {
  console.log("Serena error:", e.message);
}

Common connectivity issues:

uvx not installed: Install with pip install uvx or pipx install uvx
npx timeout: Network issues or npm registry problems
API key missing: Check environment variables are set

3. Registry Integrity

Verify YAML files are valid:

cd ${CLAUDE_PLUGIN_ROOT}
# Count tool definitions
find registry -name "*.yaml" | wc -l
# Should be ~102 files

# Check for syntax errors
npm run extract 2>&1 | grep -i error

If registry is corrupted:

rm -rf registry/
npm run extract

4. Workspace State

Check workspace directory:

cd ${CLAUDE_PLUGIN_ROOT}
ls -la workspace/
du -sh workspace/  # Check disk usage

Clean up old MCP results:

// In execute_code:
const deleted = await workspace.cleanupMcpResults(3600000); // 1 hour
console.log("Cleaned up", deleted, "old result files");

5. Serena Health (Critical)

Both Serena instances must be working:

Registry Serena (powers search_tools):

# Test semantic search
search_tools({ query: "diagram", limit: 3 })
# Should return gemini or shadcn tools

Sandbox Serena (available in execute_code):

const symbols = await serena.find_symbol({ name_path: "workspace" });
console.log("Found symbols:", symbols.content?.length || 0);

If Serena fails:

Check uvx is installed: which uvx
Check Python 3.10+: python3 --version
Try manual start: uvx --from git+https://github.com/oraios/serena serena start-mcp-server

Common Issues

Issue: "search_tools returns no results"

Causes:

Registry YAML files missing or corrupted
Serena not indexing registry directory
Query terms don't match any tool descriptions

Fix:

npm run extract   # Regenerate registry
npm run build     # Rebuild
# Restart Claude Code

Issue: "execute_code times out"

Causes:

MCP server slow to connect (first use)
Long-running operation exceeds timeout
Infinite loop in code

Fix:

Increase timeout: execute_code({ code: "...", timeout: 60000 })
Split into smaller operations
Check for infinite loops

Issue: "MCP client returns null"

Causes:

Server failed to start
Environment variable missing
Package not found (npx/uvx issue)

Fix:

# Check environment variables
echo $GEMINI_API_KEY
echo $APIFY_TOKEN

# Test server manually
npx -y @rlabs-inc/gemini-mcp

Issue: "Path traversal blocked"

Cause: Attempting to access files outside workspace.

Fix: All workspace paths must be relative and within ./workspace/:

// Wrong
await workspace.read("/etc/passwd");
await workspace.read("../package.json");

// Right
await workspace.read("data/file.txt");

Issue: "Console output truncated"

Cause: Output exceeds 500 character limit.

Fix: Keep logs concise or save verbose output to workspace:

// Instead of:
console.log(JSON.stringify(largeData, null, 2));

// Do:
await workspace.writeJSON("output.json", largeData);
console.log("Saved to output.json");

Log Locations

MCP Server Stderr:

# Claude Code captures MCP stderr
# Check Claude Code's debug output
claude --debug

Audit Log:

// In execute_code, MCP calls are logged
// Access via getAuditLog() in clients.ts (internal only)

Test Suite Details

Test File	Tests	Coverage
`tests/unit/workspace.test.ts`	13	Path traversal, read/write, JSON, directories
`tests/unit/clients.test.ts`	6	Server configs, client management
`tests/unit/search.test.ts`	10	Tool loading, search, pagination
`tests/integration/execute-code.test.ts`	14	Execution, workspace access, MCP proxies

Run specific test file:

npm test -- tests/unit/workspace.test.ts

Run with verbose output:

npm test -- --verbose

Nuclear Option: Full Reset

If nothing else works:

cd ${CLAUDE_PLUGIN_ROOT}

# Clean everything
rm -rf node_modules dist registry workspace/mcp-results

# Reinstall and rebuild
npm install
npm run extract
npm run build

# Restart Claude Code

Source Code Reference

${CLAUDE_PLUGIN_ROOT}/tests/ - All test files
${CLAUDE_PLUGIN_ROOT}/src/sandbox/clients.ts - Client lifecycle
${CLAUDE_PLUGIN_ROOT}/src/search.ts - Search implementation
${CLAUDE_PLUGIN_ROOT}/src/sandbox/runtime.ts - Execution engine

te-doctor

Tool Executor Diagnostics

Quick Health Check

Diagnostic Checklist

1. Build Status