Opt-in modern protocol negotiation for stdio MCP servers

[RhysSullivan]

Addresses a user report (tested on 1.5.41): the remote Streamable HTTP client negotiates spec 2026-07-28, but spawned stdio servers always opened with the legacy 2025 initialize handshake, so an SDK v2 server with its legacy lane disabled could not connect.

Stdio integrations now accept versionNegotiation: "auto" (addServer payload, SDK input, stored config) to probe server/discover and fall back to initialize on legacy servers. The default stays legacy per the SDK's own stdio guidance: the auto probe spawns a short-lived sibling process per connect and stalls for the probe timeout on silent legacy servers, which is the wrong default for spawn-per-call CLI servers.

The connect handshake span records the negotiated era (plugin.mcp.protocol_era) so integration authors can verify modern vs legacy from traces.

Tests: stdio-negotiation.test.ts runs the report's acceptance case against a real SDK v2 server with legacy: "reject" (auto connects modern, lists and calls tools; the default handshake fails; a both-era server stays legacy by default). The stdio e2e scenario now also adds an auto-mode server and proves fallback discovery end to end.

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