v2 - clean deprecated methods and exports

[KKonstantinov]

Clean deprecated method signature and some exports previously used for backwards compatibility

Motivation and Context

• This is a v2 cleanup that removes deprecated, backwards-compat registration APIs on McpServer (.tool, .prompt, .resource) and migrates usage to the explicit registerTool, registerPrompt, and registerResource APIs.
• Simplifies the public API surface and avoids ambiguous overloads (particularly around tool schema vs annotations), while keeping the supported registration style consistent across tools/resources/prompts.
• Removes deprecated @modelcontextprotocol/core exports/types that were retained as aliases during spec/API transitions.

How Has This Been Tested?

• Updated unit and integration tests to use the new registration APIs.
• Suggested local verification:
  • pnpm test:all
  • pnpm check:all

Breaking Changes

• Removed deprecated McpServer.tool(), McpServer.prompt(), and McpServer.resource() methods. Use registerTool, registerPrompt, and registerResource instead.
• Registration signatures are now options-object based:
  • Tools: registerTool(name, { description?, inputSchema?, outputSchema?, annotations?, execution? }, handler) (use {} when no options are needed).
  • Prompts: registerPrompt(name, { description?, argsSchema? }, handler) (use {} when no options are needed).
  • Resources: registerResource(name, uriOrTemplate, metadata, handler) (use {} when no metadata is needed).
• Removed deprecated @modelcontextprotocol/core exports/types (update imports to the non-deprecated names):
  • isJSONRPCResponse (use isJSONRPCResultResponse / isJSONRPCResponseSchema as appropriate)
  • JSONRPCErrorSchema (use JSONRPCErrorResponseSchema)
  • isJSONRPCError (use isJSONRPCErrorResponse)
  • ResourceReferenceSchema / ResourceReference (use ResourceTemplateReferenceSchema / ResourceTemplateReference)
  • JSONRPCError (use JSONRPCErrorResponse)

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

• Includes changesets to bump @modelcontextprotocol/{core,server,node,test-integration} after removal of deprecated APIs.
• Migrates examples and tests to the register* APIs (e.g. examples/server/src/ssePollingExample.ts, server/node middleware tests, and integration tests).

[changeset-bot]

🦋 Changeset detected

Latest commit: a6a3c68

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

This PR includes changesets to release 6 packages

Name	Type
@modelcontextprotocol/node	Patch
@modelcontextprotocol/test-integration	Patch
@modelcontextprotocol/server	Patch
@modelcontextprotocol/core	Patch
@modelcontextprotocol/express	Patch
@modelcontextprotocol/hono	Patch

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@modelcontextprotocol/client

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@modelcontextprotocol/express

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@modelcontextprotocol/hono

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@modelcontextprotocol/node

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commit: a6a3c68