Gitlab::Shell works on shard name, not path
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
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