Upgrade server and VS Code extension dependencies

[Copilot]

Updates npm dependencies for the server and VS Code extension while avoiding breaking major-version upgrades.

Changes

• Upgrade compatible runtime and development dependencies.
• Retain current major versions of Node types, TypeScript, and Zod.
• Refresh the npm lockfile and transitive dependencies.
• Rebuild the tracked server distribution and source map.

[github-actions]

Dependency Review

The following issues were found:

• ✅ 0 vulnerable package(s)
• ✅ 0 package(s) with incompatible licenses
• ✅ 0 package(s) with invalid SPDX license definitions
• ⚠️ 3 package(s) with unknown licenses.

View full job summary

[Copilot]

Pull request overview

This PR updates npm dependencies across the server workspace and the VS Code extension workspace, refreshing the lockfile to pick up newer compatible versions while keeping key major versions stable.

Changes:

• Bump server runtime/dev dependencies (e.g., @modelcontextprotocol/sdk, js-yaml, sql.js, tooling like eslint/prettier/typescript-eslint).
• Bump root workspace dev tooling versions to match (eslint, prettier, typescript-eslint).
• Refresh package-lock.json to reflect updated direct and transitive dependency resolution (including test tooling updates for the VS Code extension).

Show a summary per file

File	Description
server/package.json	Updates server direct dependencies and dev tooling versions.
package.json	Updates root/workspace dev tooling versions.
package-lock.json	Regenerates lockfile with updated resolved versions for workspaces and transitive deps.
extensions/vscode/package.json	Updates VS Code extension dev tooling and test harness dependencies.

Review details

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• Files reviewed: 3/6 changed files
• Comments generated: 0
• Review effort level: Lite