Add Serena gateway tests and document stdio/HTTP behavioral differences

[Copilot]

Created test suite to validate Serena MCP server behavior through the MCP gateway, revealing fundamental protocol differences between stdio and HTTP transports.

Changes

• New test script test/serena-mcp-tests/test_serena_via_gateway.sh

  • Launches gateway container with Serena backend
  • Implements proper MCP handshake (initialize + notifications/initialized)
  • Parses SSE responses from gateway
  • 23 test cases covering initialization, tools listing, and tool execution

• Makefile targets

  • make test-serena-gateway - Run gateway tests
  • Updated make test-serena description to clarify direct connection

• Documentation

  • GATEWAY_TEST_FINDINGS.md - Behavioral analysis
  • IMPLEMENTATION_SUMMARY.md - Implementation details
  • Updated README.md with usage instructions

Key Finding

Stdio-based MCP servers like Serena require persistent connection state:

# Direct stdio: Single persistent stream (68/68 tests pass)
echo '{"method":"initialize"...}
{"method":"notifications/initialized"}
{"method":"tools/call"...}' | docker run -i serena

# HTTP gateway: Independent stateless requests (7/23 tests pass)
curl -X POST /mcp/serena -d '{"method":"initialize"...}'        # ✓ Works
curl -X POST /mcp/serena -d '{"method":"notifications/..."}'    # ✓ Works  
curl -X POST /mcp/serena -d '{"method":"tools/call"...}'        # ✗ "invalid during session initialization"

Each HTTP request creates a new session. Serena rejects tool calls outside the initialization stream. This is expected given current gateway architecture - tests document the limitation and provide regression baseline for future session persistence features.

Test Results

Working: Container startup, initialization handshake, error handling
Limited: Tool execution requires connection-level session state not maintained across HTTP requests

Both test suites can run independently for comparison.

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