repository: use `git_repository_item_path`
The recent introduction of the commondir variable of a repository requires callers to distinguish whether their files are part of the dot-git directory or the common directory shared between multpile worktrees. In order to take the burden from callers and unify knowledge on which files reside where, the `git_repository_item_path` function has been introduced which encapsulate this knowledge. Modify most existing callers of `git_repository_path` to use `git_repository_item_path` instead, thus making them implicitly aware of the common directory.
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