Fix broken Gitaly integration tests

Gitaly started to require Repository information for certain commands like upload-pack, upload-archive, and receive-pack: gitaly@6b32a64b.

However, gitlab-shell tests are sending git_object_directory and git_alternate_object_directories that do not exist.

To fix the tests, we set those to an existing directory in the created repository.

Related to !693 (comment 1166683308) and Slack thread (internal).