Disable metadata creation hack in commit service tests

This commit amends the diff service's tests to not rely on Praefect's metadata force creation hack. The hack creates metadata for repositories when Praefect first sees a request for the repository. This has potential to hide problems in tests and doesn't match the production scenario. To prepare for removing the hack entirely, this commit refactors the tests to create the test repositories through the API rather than placing them directly in the storage.

In some tests, the tested branch was changed from 'master' to 'main' as Gitaly creates repositories with 'main' as the default branch.

Related to: #4019 (closed)