Set project_id for existing orphaned packages dependencies

Context

We're preparing the packages_dependencies for adding the sharding key project_id.

In Set project_id when creating Packages::Dependency (!161039 - merged) we added the changes to set project_id for new dependencies, and in Add migration to backfill project_id for packag... (!161798 - merged) to backfill project_id for existing dependencies that have the linked packages dependency links where we can use project_id.

Now we got the case when orphaned packages dependencies (the dependencies that don't have any linked dependency links) and should be removed with the Packages::Cleanup::DeleteOrphanedDependenciesWorker, in the meantime becoming used by newly uploaded packages and dependency links, and thus becoming not orphaned, but without project_id.

What does this MR do and why?

This MR changes the Packages::CreateDependencyService service to set project_id for existing orphaned packages dependencies, when they're re-used.

MR acceptance checklist

Please evaluate this MR against the MR acceptance checklist. It helps you analyze changes to reduce risks in quality, performance, reliability, security, and maintainability.

Screenshots or screen recordings

No.

How to set up and validate locally

1. Create orphaned dependency without project using rails console

   FactoryBot.create(:packages_dependency, name: 'axios', version_pattern: '^1.7.5' project: nil)

   Note: note down the ID, we'll need it on the verification step.

2. Create a new npm package that uses axios@1.7.5

   npm init
   
   # Now edit package's name (if needed) and add authentication to `.nmprc` [docs](https://docs.gitlab.com/ee/user/packages/npm_registry/#publishing-a-package-via-the-command-line)
   
   # Install dependency and publish a package to the registry.
   npm i axios@1.7.5
   npm publish

3. Verify that previously orphaned dependency now has project_id set.

   Packages::Dependency.find(dependency_id)

Related to #465276 (closed)