remove references to npm, clean up package manager usage in workspaces

[josefaidt]

Motivation and Context

The main branch includes usage of both pnpm and npm, where pnpm seems more prevalent. This PR:

1. removes all references to npm throughout the repo
2. removes package-lock.json, consolidates on pnpm usage
3. consolidates usage of packageManager to the repo root, it is not needed in workspace packages
4. removes pnpm entries from engines, the packageManager key is sufficient
5. removes manage-package-manager-versions from .npmrc, versions are now consolidated to root and can be managed by corepack -- contributing guide states to use corepack
6. removes unused start npm scripts that invoke npm start server -- these files are not found in workspace packages
7. migrates check npm scripts to use pnpm as the package manager

I'd also suggest considering further cleanup of the gitignore file. I removed what I thought was unnecessary given the state of the repo and package manager of choice, but there are still plenty of entries that do not seem to be needed (like .node_repl_history and .lock-wscript)

How Has This Been Tested?

confirmed scripts still work as expected

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

[changeset-bot]

🦋 Changeset detected

Latest commit: c23bf00

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

This PR includes changesets to release 6 packages

Name	Type
@modelcontextprotocol/express	Patch
@modelcontextprotocol/hono	Patch
@modelcontextprotocol/node	Patch
@modelcontextprotocol/client	Patch
@modelcontextprotocol/server	Patch
@modelcontextprotocol/core	Patch

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[pkg-pr-new]

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@modelcontextprotocol/client

npm i https://pkg.pr.new/modelcontextprotocol/typescript-sdk/@modelcontextprotocol/client@1534

@modelcontextprotocol/server

npm i https://pkg.pr.new/modelcontextprotocol/typescript-sdk/@modelcontextprotocol/server@1534

@modelcontextprotocol/express

npm i https://pkg.pr.new/modelcontextprotocol/typescript-sdk/@modelcontextprotocol/express@1534

@modelcontextprotocol/hono

npm i https://pkg.pr.new/modelcontextprotocol/typescript-sdk/@modelcontextprotocol/hono@1534

@modelcontextprotocol/node

npm i https://pkg.pr.new/modelcontextprotocol/typescript-sdk/@modelcontextprotocol/node@1534

commit: c23bf00