Convert run variant analysis command to new commands package

[koesie10]

This replaces the run variant analysis commands by an implementation based on the new commands package. There should be no changes in behaviour.

Based on #2157

Checklist

• CHANGELOG.md has been updated to incorporate all user visible changes made by this pull request.
• Issues have been created for any UI or other user-facing changes made by this pull request.
• [Maintainers only] If this pull request makes user-facing changes that require documentation changes, open a corresponding docs pull request in the github/codeql repo and add the ready-for-doc-review label there.

[koesie10]

I'd have preferred to not import from vscode in the src/common directory, but importing a type should be fine. We could also create an interface that defines the necessary properties to avoid importing from vscode here, but we'd need to find out which methods on Uri in command arguments are being used. For this command, it's just fsPath, but for others there may be more.