fix: improve error handling and add guard check to deserializeMessage

[saharis9988]

This PR adds a guard check to the MCP TypeScript SDK’s stdio message deserialization logic to prevent JSON parsing errors when non-JSON RPC lines are received on the stdio stream.

Motivation and Context

The MCP SDK currently assumes that every line received over stdio is a valid JSON-RPC message.
However, there are scenarios where non-JSON or otherwise invalid JSON RPC data may be written to stdout
whether from the runtime environment, external tooling, or other processes that share the same output stream.
When these invalid messages reach the SDK, the deserializer attempts to parse them and throws a SyntaxError, which impacts overall stability.

This update adds a safeguard that gracefully skips any line that is not valid JSON, making the stdio transport more robust and tolerant of incidental or malformed output on the stream.

How Has This Been Tested?

I added a unit test covering this scenario to ensure that non-JSON RPC valid input is gracefully ignored by the stdio transport.
I'm going to build the MCP Inspector against the RC version of this fix and verify that the issue is no longer reproducible and that invalid JSON-RPC messages are handled safely without causing errors.

Breaking Changes

None.
This change is fully backward compatible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the MCP Documentation
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have added or updated documentation as needed

Additional context

reference to the issue #700

[pkg-pr-new]

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npm i https://pkg.pr.new/modelcontextprotocol/typescript-sdk/@modelcontextprotocol/sdk@1225 

commit: 07b48df

[KKonstantinov]

Thank you for your work on this.

Leaving one comment with a question

[KKonstantinov]

Understand the SynthaxError, however previously, the SDK did not return null if JSONRPCMessageSchema.parse threw, why the change?

[saharis9988]

Hey @KKonstantinov, thanks for the review 🙏
I agree - the SDK shouldn’t swallow JSONRPCMessageSchema.parse errors, since throwing in those cases is intentional and important for detecting real protocol violations.
My initial thought was to ignore all invalid JSON-RPC messages, but that would indeed mask real protocol issues.
I’ve updated the fix so that only non-JSON lines are skipped while invalid JSON-RPC messages continue to throw, and I also added an additional test to cover this use case 👍

[saharis9988]

UPDATE:
While testing the previous implementation in the MCP Inspector, I noticed that when an invalid JSON message appeared at the start of a buffer chunk, the SDK discarded all subsequent lines in that chunk as well.
In the new implementation, invalid JSON lines are filtered out at append time, ensuring the buffer remains intact.
After testing this updated approach in the Inspector with the RC version, no errors are thrown and everything works as expected.
Integration tests have been added as well..

[saharis9988]

@felixweinberger @KKonstantinov
Is there anything blocking us from moving forward with this PR?
The RC version was tested in the inspector and the issue is resolved.
I’m personally waiting on this fix.. can we take another look and move toward reviewing and merging it?
Thanks! 🙏