fix returning all items that match query in get_compounds(),get_reactions()

(1) Fixed the get_compounds() and get_reactions() methods to return all items that match the query.  Previously the methods returned the first match but there can be multiple items in the biochemistry database that are a match.  (2) Added --biochem and --biochemws arguments to the fba-getcompounds and fba-getreactions commands to take advantage of support already provided by the server methods. (3) Updated the export_genome() method to support a 'genomeTO' format to return the genome in the format used by the genome annotation service.