v2: pnpm audit fixes

[KKonstantinov]

v2 - version bumps / audit fixes.

@modelcontextprotocol/conformance needs to be bumped via modelcontextprotocol/conformance#108 as well, as it uses the 1.25.1 v1 version, which has a CVE gainst it.

Motivation and Context

How Has This Been Tested?

Breaking Changes

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

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Latest commit: 1c3e5ee

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[pkg-pr-new]

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@modelcontextprotocol/client

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@modelcontextprotocol/server

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@modelcontextprotocol/express

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@modelcontextprotocol/hono

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@modelcontextprotocol/node

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commit: 1c3e5ee