More codepaths become aware of working with in-core repository
instance other than the default "the_repository".

* nd/the-index: (22 commits)
  rebase-interactive.c: remove the_repository references
  rerere.c: remove the_repository references
  pack-*.c: remove the_repository references
  pack-check.c: remove the_repository references
  notes-cache.c: remove the_repository references
  line-log.c: remove the_repository reference
  diff-lib.c: remove the_repository references
  delta-islands.c: remove the_repository references
  cache-tree.c: remove the_repository references
  bundle.c: remove the_repository references
  branch.c: remove the_repository reference
  bisect.c: remove the_repository reference
  blame.c: remove implicit dependency the_repository
  sequencer.c: remove implicit dependency on the_repository
  sequencer.c: remove implicit dependency on the_index
  transport.c: remove implicit dependency on the_index
  notes-merge.c: remove implicit dependency the_repository
  notes-merge.c: remove implicit dependency on the_index
  list-objects.c: reduce the_repository references
  list-objects-filter.c: remove implicit dependency on the_index
  ...