EE: Ensure that template is used once

What does this MR do?

EE version of this CE MR: https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/27511

Today we allow the specification of:

include:
  - template: Ruby.gitlab-ci.yml

However, when evaluating the usage of Ruby.gitlab-ci.yml we iterate through all folders that are visible from UI perspective. It means that the same file can exist multiple times in different folders and we have no way to make it clear (except passing path with the folder) to ensure that Ruby.gitlab-ci.yml, if used in this form, is the template that you want to use.

Related to https://gitlab.com/gitlab-org/gitlab-ce/issues/60144

Does this MR meet the acceptance criteria?

Conformity

• Changelog entry
• Code review guidelines
• Style guides