Merge branch 'ps/setup-wo-the-repository'

Many uses of the_repository has been updated to use a more
appropriate struct repository instance in setup.c codepath.

* ps/setup-wo-the-repository:
  setup: stop using `the_repository` in `init_db()`
  setup: stop using `the_repository` in `create_reference_database()`
  setup: stop using `the_repository` in `initialize_repository_version()`
  setup: stop using `the_repository` in `check_repository_format()`
  setup: stop using `the_repository` in `upgrade_repository_format()`
  setup: stop using `the_repository` in `setup_git_directory()`
  setup: stop using `the_repository` in `setup_git_directory_gently()`
  setup: stop using `the_repository` in `setup_git_env()`
  setup: stop using `the_repository` in `set_git_work_tree()`
  setup: stop using `the_repository` in `setup_work_tree()`
  setup: stop using `the_repository` in `enter_repo()`
  setup: stop using `the_repository` in `verify_non_filename()`
  setup: stop using `the_repository` in `verify_filename()`
  setup: stop using `the_repository` in `path_inside_repo()`
  setup: stop using `the_repository` in `prefix_path()`
  setup: stop using `the_repository` in `is_inside_work_tree()`
  setup: stop using `the_repository` in `is_inside_git_dir()`
  setup: replace use of `the_repository` in static functions

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