Add MCP stdio transport smoke tests (Phase 5)

Tests the actual agent handshake path that Claude Code, OpenCode, etc. use:
- 5a-d: initialize → notifications/initialized → tools/list via bare JSONL
- 5e: Full tool call round-trip (index + search) via JSON-RPC
- 5f: Content-Length framing (OpenCode compatibility)

Uses portable background process + kill instead of timeout command
(not available on all macOS configurations).