[v1.x] fix(server): close StdioServerTransport when stdin ends or closes

[maxymlyskov]

Backport of #2494 for #2002 on v1.x.

On v1.x, StdioServerTransport.start() listens for stdin data and error and nothing else (src/server/stdio.ts#L53-L63). So when the client hangs up the pipe, the transport never closes and onclose never fires. A server that frees a timer or pool in onclose keeps running with no parent. #2002 has 6 of them piling up in ~17 hours (all PPID=1) and another report of 7 in 5 days on 1.29.0, and its triage comment reproduced the same code on v1.x.

Driver: a real child server holding a setInterval it clears in onclose. It completes initialize, then child.stdin.end(), no signal:

### v1.x c2ce0031 (Windows 11, Node v22.12.0)
RESULT: server pid 22588 STILL RUNNING 10009 ms after stdin EOF, onclose never fired -> SIGKILL
### this branch (Windows 11, Node v22.12.0)
  [child stderr] server: onclose fired (#1), keep-alive released
RESULT: server exited code=0 10 ms after stdin EOF
### v1.x c2ce0031 (WSL2 Linux, Node v22.22.0)
RESULT: server pid 496 STILL RUNNING 10011 ms after stdin EOF, onclose never fired -> SIGKILL
### this branch (WSL2 Linux, Node v22.22.0)
  [child stderr] server: onclose fired (#1), keep-alive released
RESULT: server exited code=0 7 ms after stdin EOF

The fix is the stdin half of #2494: end and close listeners that close the transport, removed again in close(), a _closed guard (today a second close() fires onclose twice), and a setImmediate close when stdin already ended or was destroyed before start().

One change a v1 user can notice: requests still in flight at stdin EOF are aborted and their responses aren't written. Same as main, and the changeset says so.

Left out: stdout error handling, send() rejecting after close and the swallow-listener sweep. On v1.x that's open #2579, which edits this file and adds its own _closed guard, so whichever lands second gets a small rebase.

Tests

• test/server/stdio.test.ts: fix(server): close StdioServerTransport when stdin ends or closes #2494's seven stdin tests, unchanged, plus one checking close() removes the end/close listeners. stdin defaults to the shared process.stdin and the _closed guard would hide a leftover listener, so nothing else catches it.
• test/integration-tests/processCleanup.test.ts + src/__fixtures__/serverWithKeepAlive.ts from fix(server): close StdioServerTransport when stdin ends or closes #2494: the child exits on its own when the client closes stdin. It takes its own 15 s timeout, since the describe uses 5 s and the zombie bound is 8 s.

On untouched v1.x, 8 of the 9 fail and the listener test passes on both:

     × server process should exit on its own when the client closes stdin 8497ms
   × should close and fire onclose when stdin ends (client hung up) 5011ms
   × should close and fire onclose when stdin closes 5010ms
   × should fire onclose when stdin was already destroyed before start() 5012ms
   × should fire onclose when stdin had already ended before start() 5014ms
   × should fire onclose assigned after start() when stdin was already dead 5005ms
   × should not fire onclose twice when close() is called after stdin ends 5014ms
   ✓ should remove its stdin end and close listeners on close 1ms
   × should still deliver messages that arrived before stdin ended 5009ms
⎯⎯⎯⎯⎯⎯⎯ Failed Tests 8 ⎯⎯⎯⎯⎯⎯⎯
AssertionError: expected 'zombie' to be +0 // Object.is equality
Error: Test timed out in 5000ms.
 Test Files  2 failed (2)
      Tests  8 failed | 1 passed | 8 skipped (17)

• npm test: 1818 passed (Windows 11 / Node 22.12)
• npm run test:e2e: 1114 passed, 1 failed. transport:stdio:shutdown-escalation fails the same way on untouched v1.x (Windows delivers no catchable SIGTERM). On WSL2 Linux / Node 22.22: 1115 passed.
• npm run typecheck, npm run lint: clean

Changeset included.

[changeset-bot]

🦋 Changeset detected

Latest commit: 5fec54b

The changes in this PR will be included in the next version bump.

Not sure what this means? Click here to learn what changesets are.

Click here if you're a maintainer who wants to add another changeset to this PR

[pkg-pr-new]

Open in StackBlitz

npm i https://pkg.pr.new/@modelcontextprotocol/sdk@2911

commit: 5fec54b