Move EE-specific files to a standalone directory

What does this MR do?

Move EE-specific files to a standalone directory

• app/{models, controllers, etc}
• lib
• app/views
• app/views/admin/monitoring/ee
• app/views/projects/protected_branches/ee
• app/views/projects/protected_tags/ee
• app/views/projects/settings/ee
• app/assets/javascripts/vue_merge_request_widget/ee
• app/assets/javascripts/protected_branches/ee
• app/assets/javascripts/protected_tags/ee
• spec
• qa

Why was this MR needed?

To make it more clear which codes are EE-specific

Does this MR meet the acceptance criteria?

• Documentation created/updated

What are the relevant issue numbers?

Closes #2902 (closed)