repository: use `git_repository_item_path`

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.