Respect locus curator list on contents page when using sets.
Expand autotagger options to define a 'new' isolate.
When using the --new_only option, isolates were tagged if they had
contigs in their sequence bin but no alleles designated/tagged.
Sometimes, however, a curator may have tagged the MLST loci manually, so
the remaining loci will not be tagged with this option. Now we have an
additional option '--new_max_alleles' to set a maximum number of
designations/tags that have to have been made before the isolate is no
longer considered new.