Cleanup leftovers in packages_dependencies table

What does this MR do and why?

MR !20549 (merged) added two tables: packages_dependencies and packages_dependency_links. When a package is deleted, packages_dependency_links rows are properly deleted but rows in packages_dependencies are kept and they can become orphans. This MR aims to clean up those orphaned packages_dependencies records.

How to set up and validate locally

1. In Rails console, create a bunch of orphaned packages_dependencies records: FactoryBot.create_list(:packages_dependency, 100)
2. Enable the feature flag : Feature.enable(:packages_delete_orphaned_dependencies_worker)
3. Run the cleanup sidekiq worker: Packages::Cleanup::DeleteOrphanedDependenciesWorker.perform_async, the orphaned records should be deleted.

MR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

• I have evaluated the MR acceptance checklist for this MR.

Database analysis

1. !113076 (comment 1297596269)
2. !113076 (comment 1322050386)

Related to #38266 (closed)

app/models/packages/dependency.rb

 # frozen_string_literal: true
 class Packages::Dependency < ApplicationRecord
+  include EachBatch
+
   has_many :dependency_links, class_name: 'Packages::DependencyLink'
 
   validates :name, :version_pattern, presence: true
@@ -41,6 +43,11 @@ def self.pluck_ids_and_names
     pluck(:id, :name)
   end
 
+  def self.orphaned
+    subquery = Packages::DependencyLink.where(Packages::DependencyLink.arel_table[:dependency_id].eq(Packages::Dependency.arel_table[:id]))
+    where_not_exists(subquery)
+  end
+
   def orphaned?
     self.dependency_links.empty?
   end