This is C equivalent of "git config --set --worktree". In other words,
it will

- write to $GIT_DIR/config in single-worktree setup

- write to $GIT_COMMON_DIR/worktrees/<x>/config.worktree or
  $GIT_COMMON_DIR/config.worktree (for main worktree)
  if extensions.worktreeConfig is enabled

- return error in multiple-worktree setup if extensions.worktreeConfig
  is not enabled.

While at there, also add repo_config_set*() for writing to
$GIT_COMMON_DIR/config.

Note, since git_config_set_multivar_in_file_gently() only invalidates
the config set of the_repository, anybody who uses these functions on
submodules must do additional invalidation if needed.