MCP: Claude Code sends legacy 'initialize' after successful modern 'server/discover', breaking modern-only servers

Bug Description

Claude Code 2.1.280 sends a legacy initialize handshake after receiving a successful server/discover response from a modern-only MCP server. Per the MCP 2026-07-28 spec, when server/discover returns a DiscoverResult with supportedVersions: ["2026-07-28"], the client should stay in modern mode and not fall back to initialize.

Steps to Reproduce

1. Configure an MCP server that only supports the 2026-07-28 protocol (e.g., Atlassian MCP server running fastmcp >= 4.0.0)
2. Connect via stdio transport with tengu_mcp_protocol_negotiation_stdio: true
3. Claude Code sends server/discover → server responds with supportedVersions: ["2026-07-28"]
4. Claude Code then sends initialize (legacy handshake)
5. Server rejects with -32022: "connection is serving the 2026-07-28 protocol; the initialize handshake is not accepted"

Expected Behavior

After a successful server/discover response indicating modern-only support, Claude Code should proceed in modern mode without sending initialize.

Actual Behavior

Claude Code falls back to initialize after a successful modern discovery, which modern-only servers reject with error -32022.

Why Some Servers Work

Servers like GitHub MCP Server (v1.3.0) reject server/discover entirely, causing Claude Code to correctly fall back to legacy initialize. The bug only manifests with servers that accept server/discover and declare themselves modern-only.

Environment

• Claude Code: 2.1.280
• OS: macOS (Darwin 25.6.0)
• Transport: stdio (via proxy)
• Failing server: Atlassian MCP (fastmcp 4.0.3, atlassian-mcp v4.0.3)
• Working server: GitHub MCP Server v1.3.0 (rejects server/discover, so legacy path works)