Move all EE-specific code to ee/ and spec/ee/ directories part 2

This is a follow up from https://gitlab.com/gitlab-org/gitlab-ee/issues/2902

We no longer have EE directory, but we still have a lot of EE specific files residing in place. Let's move all of them, too.

• Migrations: https://gitlab.com/gitlab-org/gitlab-ee/issues/2902#note_36442081 $1671366
• Files in app $1671365
• Files in lib $1671367
• Geo: https://gitlab.com/gitlab-org/gitlab-ee/issues/3148
• spec/models/project_services/kubernetes_service_ee_spec.rb
• spec/requests/api/variables_ee_spec.rb
• spec/controllers/projects/issues_controller_ee_spec.rb
• spec/controllers/projects/merge_requests/creations_controller_ee_spec.rb
• spec/controllers/projects/settings/repository_controller_ee_spec.rb
• spec/controllers/projects/merge_requests_controller_ee_spec.rb
• spec/features/issues/sub_nav_ee_spec.rb
• spec/features/variables_ee_spec.rb
• spec/support/protected_tags/access_control_ee_spec.rb
• spec/support/shared_examples/features/protected_branches_access_control_ee.rb
• spec/javascripts/filtered_search/filtered_search_token_keys_issues_ee_spec.js
• app/views/layouts/nav/_admin_ee.html.haml
• app/assets/images/emoji/flag_ee.png (Please don't move the Estonian flag 🇪🇪)
• app/assets/javascripts/filtered_search/filtered_search_token_keys_issues_ee.js
• ee/app/views/admin/monitoring/ee
• ee/app/views/devise/shared/ee
• ee/app/views/groups/ee
• ee/app/views/projects/ee
• ee/app/views/projects/protected_branches/ee
• ee/app/views/projects/protected_tags/ee
• ee/app/views/projects/settings/ee
• ee/app/views/projects/variables/ee
• ee/app/views/shared/issuable/form/ee
• ee/app/views/shared/members/ee

And those filenames don't contain EE at all.