[Server] Expire timed out client requests in Protocol::checkResponse()

[Arslan-TR]

Fixes #561

The unknown-ID half of the issue is already handled by handleResponse() on main; this covers the other half.

Problem

When a request to the client (elicitation, sampling) timed out, the polling loops of StreamableHttpTransport and StdioTransport resumed the fiber with a Request timed out error but never removed the entry from _mcp.pending_requests. Only Protocol::checkResponse() did that, and only for answers. So the entry stayed in the session until it ended, and a fiber that suspended again was resumed with the same stale timeout once more.

Change

• Protocol::checkResponse() now returns the Request timed out error for a request past its timeout and drops its pending entry, like an answer does. An answer that is already stored still wins over the timeout.
• The timeout branches (and their copies of the timestamp/timeout bookkeeping) are removed from both transports; checkForResponse() keeps its signature.
• The expiry reloads the session before saving, so it does not write back a stale snapshot over what another stream stored in the meantime (ProtocolSessionRaceTest covers that case; its timed out request now returns the error instead of null). The general read-modify-write race stays with [Server][Streamable HTTP] Concurrent requests in the same session can overwrite queued responses and cause stale/unknown message IDs #275.
• StreamableHttpTransport loses its $clock constructor argument, as the transport no longer compares timestamps itself. It was added after v0.8.1, so it is not in a release yet. Protocol uses time(), like handleResponse() already does.
• CHANGELOG entry added.

Tests

New in ProtocolTest: the timed out request is reported once and only its entry is dropped, a request within its timeout stays pending, a stored answer beats the timeout, a late answer after the reported timeout is dropped, and a stream stops polling a request that timed out. The StreamableHttpTransport test that relied on the injected clock now checks that the polling loop resumes the fiber with the error the response finder returns.

ProtocolTest::testCheckResponseReportsTimedOutRequestAndDropsItsPendingEntry, testAnswerAfterReportedTimeoutIsDropped, testStreamStopsPollingTimedOutRequest and the updated ProtocolSessionRaceTest case fail without the src/ change.

Ran locally: phpunit unit suite, phpstan (no errors), php-cs-fixer on the changed files. The unit suite still has failures that are the same without this change (FileSessionStoreTest permission tests, JwtTokenValidatorTest, HttpTransportListenTest, on Windows). The integration tests that spawn a stdio server did not finish here, and DualEraEndpointTest::testAsksForInput fails identically on main; I did not run the interop/conformance suites.