Add package dependencies cleanup migration

Those with dependency_type 5 should be removed

db/migrate/20200210135504_remove_packages_deprecated_dependencies.rb

+# frozen_string_literal: true
+
+class RemovePackagesDeprecatedDependencies < ActiveRecord::Migration[6.0]
+  DOWNTIME = false
+
+  def up
+    execute('DELETE FROM packages_dependency_links WHERE dependency_type = 5')
+  end
+
+  def down
+    # There is nothing to do to reverse this migration
+  end
+end

ee/changelogs/unreleased/10io-remove-deprecated-package-dependencies.yml

+---
+title: Cleanup deprecated package dependency links
+merge_request: 24868
+author:
+type: fixed

spec/migrations/remove_packages_deprecated_dependencies_spec.rb

+# frozen_string_literal: true
+
+require 'spec_helper'
+require Rails.root.join('db', 'migrate', '20200210135504_remove_packages_deprecated_dependencies.rb')
+
+describe RemovePackagesDeprecatedDependencies, :migration do
+  let(:projects) { table(:projects) }
+  let(:packages) { table(:packages_packages) }
+  let(:dependency_links) { table(:packages_dependency_links) }
+  let(:dependencies) { table(:packages_dependencies) }
+
+  before do
+    projects.create!(id: 123, name: 'gitlab', path: 'gitlab-org/gitlab-ce', namespace_id: 1)
+    packages.create!(id: 1, name: 'package', version: '1.0.0', package_type: 4, project_id: 123)
+    5.times do |i|
+      dependencies.create!(id: i, name: "pkg_dependency_#{i}", version_pattern: '~1.0.0')
+      dependency_links.create!(package_id: 1, dependency_id: i, dependency_type: 5)
+    end
+    dependencies.create!(id: 10, name: 'valid_pkg_dependency', version_pattern: '~2.5.0')
+    dependency_links.create!(package_id: 1, dependency_id: 10, dependency_type: 1)
+  end
+
+  it 'removes all dependency links with type 5' do
+    expect(dependency_links.count).to eq 6
+
+    migrate!
+
+    expect(dependency_links.count).to eq 1
+  end
+end