Fix save notes in metadata

Several commands have a --notes parameter for the user to provide information about the analysis being run but the notes were not being saved.  Updated the save_objects() method in KBaseStore.pm to look at the input parameters stored in the provenance data and if there is a "notes" parameter the notes are also set in the meta data for the object being saved.  The user can then view the notes in the workspace browser.  Saving the notes is implicitly done for any command that has a "notes" parameter.  There is a limit to the size of the provenance data so a very long string in the "notes" parameter could cause an error when saving the object.  Also updated three command scripts that were missing the "notes" parameter in the translation dictionary.