chore: upgrade sample-servers to MCP SDK 1.25.3 and zod 4

[xiaoyijun]

Summary

Upgrade sample-servers to use the latest MCP SDK 1.25.3 and zod 4.

Changes:

• Upgrade @modelcontextprotocol/sdk to ^1.25.3
• Upgrade zod to ^4.3.5 for both mcp-auth and sample-servers
• Use StreamableHTTPServerTransport instead of SSEServerTransport
• Use server.registerTool() instead of server.tool()
• Use protectedResourceMetadataRouter() for todo-manager (protected resource mode)
• Add MCP_RESOURCE_IDENTIFIER env var for todo-manager
• Update README with new environment variables
• Add .env.example file

Testing

tested locally

Checklist

• .changeset
• unit tests
• integration tests
• necessary TSDoc comments

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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