[Server] Concurrent requests corrupt the session file in FileSessionStore, crashing Session::readData() with JsonException

Describe the bug

Under PHP-FPM, two concurrent requests carrying the same Mcp-Session-Id can leave the session file empty (0 bytes). The next read of that session throws an uncaught JsonException out of Session::readData(), and the server answers -32603 for a tool call that had already completed successfully — the tool ran, its response was queued in the session, and then the response could not be retrieved.

Two independent defects combine here; each is a necessary condition.

1. FileSessionStore::write() uses a fixed temporary filename. $tmp = $path.'.tmp'; is identical for every concurrent writer of the same session, and file_put_contents() opens the stream in w mode — so truncation happens before LOCK_EX is acquired. One process can therefore rename() a temp file that another process has just truncated to 0 bytes, publishing an empty session file. The // Atomic move comment applies to rename() alone; the operation as a whole is not atomic because the temp name is shared. The copy() fallback has the same problem (it truncates the destination and then streams into it), and read() takes no LOCK_SH.

2. Session::readData() does not guard against an empty string. Only false is handled, so '' reaches json_decode(..., JSON_THROW_ON_ERROR):

$rawData = $this->store->read($this->id);
if (false === $rawData) { return $this->data = []; }        // only false is handled
$decoded = json_decode($rawData, true, flags: \JSON_THROW_ON_ERROR);   // throws on ''
if (!\is_array($decoded)) { return $this->data = []; }      // unreachable for ''

FileSessionStore::read() returns '' for a zero-byte file — it returns false only when the file is missing, expired, or unreadable. This half is store-agnostic: any store that can return an empty string triggers it.

To Reproduce

Steps to reproduce the behavior:

1. Run a server on PHP-FPM with StreamableHttpTransport and FileSessionStore (handshake era).
2. POST an initialize request without a session id; take Mcp-Session-Id from the response headers.
3. POST notifications/initialized with that header.
4. Deterministic variant — truncate the session file by hand: : > <session-dir>/<session-id> (or write invalid JSON: printf '{"a":' > <session-dir>/<session-id>).
5. POST tools/list with the same Mcp-Session-Id. The request fails with -32603 and the JsonException below.
6. Concurrency variant (shows the actual cause rather than the symptom) — instead of step 4, fire ~40 parallel tools/list POSTs sharing one Mcp-Session-Id, e.g. seq 40 | xargs -P 8 -I{} curl -s -o /dev/null -w '%{http_code}\n' -X POST ..., and repeat a few rounds. Occasional requests fail with -32603.

Expected behavior

1. Concurrent writes to the same session never publish a partial or empty session file.
2. An empty or undecodable payload from the store degrades to an empty session instead of a fatal error. The existing !\is_array($decoded) branch already shows this is the intended behaviour — it is simply unreachable while JSON_THROW_ON_ERROR fires first.

Logs

JsonException: Syntax error in src/Server/Session/Session.php:168
#0 Session.php(168): json_decode('', true, 512, 4194304)
#1 Session.php(53):  Mcp\Server\Session\Session->readData()
#2 Protocol.php(517): Mcp\Server\Session\Session->get(Array, Array)
#3 BaseTransport.php(81): Mcp\Server\Protocol->consumeOutgoingMessages(Symfony\Component\Uid\UuidV4)
#4 StreamableHttpTransport.php(218): Mcp\Server\Transport\BaseTransport->getOutgoingMessages(...)
#5 StreamableHttpTransport.php(202): ...->createJsonResponse()
#6 StreamableHttpTransport.php(437): ...->handlePostRequest('{"jsonrpc":"2.0...')
#7 Server.php(67): Mcp\Server\Transport\StreamableHttpTransport->listen()

Additional context

Why the exception escapes every catch block. The crash happens in Protocol::consumeOutgoingMessages(), which builds a fresh Session instance:

// Protocol.php:516
$session = $this->sessionManager->createWithId($sessionId);
$queue = $session->get(self::SESSION_OUTGOING_QUEUE, []);   // second, independent disk read

A single POST therefore reads the session file twice, through two objects that share no memory — and the second read happens after the request's own save() at Protocol.php:223. That second read is reached from BaseTransport::getOutgoingMessages() while the response is being built, which is outside Protocol::processInput()'s try/catch (that one wraps only doProcessInput()); Server::run() has just try/finally. The exception propagates out of Server::run() into the application's own error handler.

Silent lost writes. After the losing process's rename() fails (its temp file is gone) and copy() fails too, write() returns false — but Session::save()'s return value is discarded at Protocol.php:223, :519, :551 and :644, so the failed write is invisible.

Where a fix would belong. Both halves look small and independent — the shared temp filename in FileSessionStore::write(), and the missing '' case in Session::readData().

One more observation, separate from the bug. Since #479, gc() skips anything whose filename is not a valid UUID, so orphaned *.tmp files are never cleaned up. Harmless at one temp file per session, but worth knowing if the temp name ever becomes unique.

Related but distinct issues. #275 (lost update on concurrent read-modify-write) and #467 (concurrent POSTs returning a JSON array). A per-session lock as proposed in #275 would incidentally prevent this crash, but would not close item 2.

Environment. mcp/sdk v0.8.1, PHP 8.5, PHP-FPM, StreamableHttpTransport with withoutModernEra(), FileSessionStore on local disk (Linux), TTL 14400 s. The same code is present on main, so this is not fixed by upgrading.

Start with src/Server/Session/Session.php and the FileSessionStore::write() and read() paths, then trace the second session read from Protocol.php through BaseTransport::getOutgoingMessages(). Reproduce the empty-file case and the parallel tools/list requests described in the issue. Done means concurrent writes do not publish empty or partial files, and empty store data is treated as an empty session without an uncaught JsonException.