Update minor dependencies

[richardkmichael]

Update packages to the latest versions permitted by their package specifier; no specifier changes. In most cases, these are minor version updates.

The exception is prettier, which needs a specifier update because it was added with a single version specifier in af16a53. There are no changes to code formatting with this update.

Motivation and Context

Lessen the burden of future maintenance by keeping the project relatively up to date. Tracking minors version ought to make it easier to do major version upgrades.

How Has This Been Tested?

1. npm ci && npm run prettier-fix && npm run lint && npm run build && npm run test && npm run test:e2e
2. Tested manually against the Everything server: npx . npx @modelcontextprotocol/servers-everything.

Breaking Changes

No

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

Regarding prettier, I reviewed git log -p -G prettier -- package.json, but didn't see why it might have be pinned to 3.3.3.

Unfortunately, these updates do not address the deprecating warnings emitted on install, which was my initial motivation. They're due to an old version of test-include being used by babel and babel-plugin-istanbul, and will be fixed when this PR lands there.

@cliffhall 👋 Recently we discussed syncing package.json with package-lock.json. I could do that as a separate PR?

[cliffhall]

👋 Recently #557 (comment) syncing package.json with package-lock.json. I could do that as a separate PR?

Are package.json and package-lock.json not in sync in this PR? I think if you just delete pacakge-lock.json and do npm install they should be. Not sure why we'd want to do it in a different PR, but I could be missing something.

[richardkmichael]

👋 Recently #557 (comment) syncing package.json with package-lock.json. I could do that as a separate PR?

Are package.json and package-lock.json not in sync in this PR? I think if you just delete pacakge-lock.json and do npm install they should be.

No they weren't. I thought I'd keep the changes simple for review and history, and previous updates hadn't been changing package.json.

Not sure why we'd want to do it in a different PR, but I could be missing something.

Not really. Since it doesn't matter technically and is just a nicety when reading package.json, I was apprehensive about distracting from this. (I find it a bit easier to review package changes when there's only a change to the lock file, since I don't need to check the operator and version.)

I revised and squashed. Let me know if this isn't what you had in mind. Thanks!

[cliffhall]

Build, test, run locally all good. LGTM! 👍