[Server] stdio parse errors use `id:""` instead of preserving the request id or returning null

[cclabadmin]

Describe the bug

When the stdio server receives JSON-RPC input that exceeds PHP's JSON nesting limit, it returns a JSON-RPC parse error with id:"".

That response is hard for clients to correlate with the original request. In the repro below, the malformed request had a numeric id such as 900512, but the server response used an empty-string id like:

{"jsonrpc":"2.0","id":"","error":{"code":-32700,"message":"Maximum stack depth exceeded"}}

The server process stayed alive and later ping requests succeeded, so this is not a crash report. The issue is the response id used for recoverable parse-error handling on stdio.

• Environment:
  • Reproduced with stable release v0.5.0 (fb2c8c2ee4ab2791239c5f534bb07bfb7589d4e8)
  • Also reproduced with a main snapshot from 2026-05-26 (293a5880e44b36c2120b114d175b6ddc4d7d1b06)
  • Transport: stdio HTTP server

To Reproduce

Steps to reproduce the behavior:

1. Start a PHP SDK MCP server over stdio. I used the discovery calculator example.
2. Complete a normal initialize request followed by notifications/initialized.
3. Send a JSON-RPC request with a numeric id and a deeply nested object value. The example below uses a nested initialize.params.capabilities object at depth 512.
4. Observe the JSON-RPC error response id.

Expected behavior

For JSON-RPC errors, the response id should be the same as the request id when the id is known. If the id cannot be determined after a parse failure, JSON-RPC error responses conventionally use null for an unknown id. Returning id:"" introduces an id value that was not present in the request and is difficult for clients to correlate.

I would expect returing the parse error with id:null if the request id is not recoverable.

Logs

-> init payload depth=512:
   {"jsonrpc":"2.0","id":900512,"method":"initialize","params":{"protocolVersion":"2025-11-25","capabilities":{... deeply nested object ...}}}

<- {"jsonrpc":"2.0","id":"","error":{"code":-32700,"message":"Maximum stack depth exceeded"}}

-> health after deep payload 512:
   {"jsonrpc":"2.0","id":7,"method":"ping","params":{}}

<- {"jsonrpc":"2.0","id":7,"result":{}}

The same id:"" parse-error behavior appeared for deeper inputs as well, including depths 1024, 2048, 4096, 8192, and 10000. The server process stayed alive.