Passthrough removal part 2: Achieve 0 passthrough types.

[KKonstantinov]

Draft PR to achieve 0 passthrough on zod types.

Supercedes #1125, which was put on hold until zod v4 and 2025-25-11 is a fact.

Motivation and Context

Passthrough was largely removed in another PR, but a few still remain.

This PR aims to remove any remaining .passthrough() from the SDK.

How Has This Been Tested?

Unit tests.

Breaking Changes

None. Bringing SDK back to full spec compliance.

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

[pkg-pr-new]

Open in StackBlitz

npm i https://pkg.pr.new/modelcontextprotocol/typescript-sdk/@modelcontextprotocol/sdk@1242

commit: a297f9d