Renamed repository management methods.

OLD:

    * Manager.add()
    * Manager.commit()
    * Manager.status()
    * Manager.revert()
    * Manager.update()

NEW:

    * Manager.add_to_repository()
    * Manager.commit_to_repository()
    * Manager.repository_status()
    * Manager.revert_from_repository()
    * Manager.update_from_repository()