Make Gitlab::Git::Repository#submodules private

What does this MR do?

Preparatory work for migrating submodule URL lookups to Gitaly.

Are there points in the code the reviewer needs to double check?

Why was this MR needed?

The less Git code we have in GitLab, and the more specific it is, the easier it is to migrate it to Gitaly.

Screenshots (if relevant)

Does this MR meet the acceptance criteria?

• Changelog entry added, if necessary
• Documentation created/updated
• API support added
• Tests
  • Added for this feature/bug
  • All builds are passing
• Conform by the merge request performance guides
• Conform by the style guides
• Branch has no merge conflicts with master (if it does - rebase it please)
• Squashed related commits together

What are the relevant issue numbers?

gitaly#329 (closed)