test: add Phase 4 database integration tests (partial)

- Add comprehensive test utilities for database testing
- Implement connection management tests for in-memory and file databases
- Add transaction tests including nested transactions and savepoints
- Test database lifecycle, error handling, and performance
- Include tests for WAL mode, connection pooling, and constraints

Part of Phase 4: Integration Testing

tests/integration/mcp-protocol/README.md

@@ -0,0 +1,53 @@
+# MCP Protocol Integration Tests
+
+This directory contains comprehensive integration tests for the Model Context Protocol (MCP) implementation in n8n-mcp.
+
+## Test Structure
+
+### Core Tests
+- **basic-connection.test.ts** - Tests basic MCP server functionality and tool execution
+- **protocol-compliance.test.ts** - Tests JSON-RPC 2.0 compliance and protocol specifications
+- **tool-invocation.test.ts** - Tests all MCP tool categories and their invocation
+- **session-management.test.ts** - Tests session lifecycle, multiple sessions, and recovery
+- **error-handling.test.ts** - Tests error handling, edge cases, and invalid inputs
+- **performance.test.ts** - Performance benchmarks and stress tests
+
+### Helper Files
+- **test-helpers.ts** - TestableN8NMCPServer wrapper for testing with custom transports
+
+## Running Tests
+
+```bash
+# Run all MCP protocol tests
+npm test -- tests/integration/mcp-protocol/
+
+# Run specific test file
+npm test -- tests/integration/mcp-protocol/basic-connection.test.ts
+
+# Run with coverage
+npm test -- tests/integration/mcp-protocol/ --coverage
+```
+
+## Test Coverage
+
+These tests ensure:
+- ✅ JSON-RPC 2.0 protocol compliance
+- ✅ Proper request/response handling
+- ✅ All tool categories are tested
+- ✅ Error handling and edge cases
+- ✅ Session management and lifecycle
+- ✅ Performance and scalability
+
+## Known Issues
+
+1. The InMemoryTransport from MCP SDK has some limitations with connection lifecycle
+2. Tests use the actual database, so they require `data/nodes.db` to exist
+3. Some tests are currently skipped due to transport issues (being worked on)
+
+## Future Improvements
+
+1. Mock the database for true unit testing
+2. Add WebSocket transport tests
+3. Add authentication/authorization tests
+4. Add rate limiting tests
+5. Add more performance benchmarks