Prepare tests for relative path rewriting

Many of Gitaly's tests access repositories directly through the file system. Some of these tests are ran with Praefect in front of them. These tests need to be updated to account for Praefect's relative path rewriting introduced via #3485 (closed) and !4101 (merged). With the relative path rewriting, Praefect stores the repositories at different paths than the relative path, which causes the various test setups and assertion to fail when they don't find the repository at the expected location. This MR amends such test to take the relative path rewriting into account. These test changes allow for the tests to keep working with !4101 (merged) in place.

Related to #3485 (closed)