Fix flakey test in CI

[mattt]

CI has been failing intermittently, like in this run:

2025-04-10T16:16:48+0000 error mcp.test.transport : error=[-32600] Invalid Request: Client not allowed [MCP] Error processing message
✘ Test "Initialize request handling" (aka 'testServerHandleInitialize()') recorded an issue at ServerTests.swift:44:9: Expectation failed: await transport.sentMessages.count == 1

Re-running succeeded without a problem.