Direct disk access is done through Gitaly now, so the legacy path was
deprecated. This path was used in Gitlab::Shell however. This required
the refactoring in this commit.
Added is the removal of direct path access on the project model, as that
lookup wasn't needed anymore is most cases.
Closes https://gitlab.com/gitlab-org/gitaly/issues/1111
This will be necessary when adding gitaly settings. This version
doesn't make any functional changes, but allows us to include this
breaking change in 9.0 and add the needed extra settings in the future
with backwards compatibility
