Genome Comparator: Create core genome alignment.
Not just all loci, or all variable loci.
Don't drop scheme cache tables before updating.
It can take a few seconds to create the cache tables - if the table is
dropped and recreated this can result in an error if somebody is
querying via the web interface at that moment.  Instead, we can create a
new table named with a random suffix, then drop the old table and rename
the new one as a single transaction.
Modify locus aliases from isolate database locus record.
Use SQL placeholders for table update pages.
Additional status flag to ignore allele designations
Sometimes there is a need to completely ignore a designation so that it
is not seen by an end user, or used in analyses, but should still remain
in the database.  Ignored designations are still visible in the curation
interface but are greyed out.
Respect ignored status of allele designations in client databases.
Migrate plugins to use Datastore::run_query instead of run_simple_query.
Datastore::run_simple_query has been deprecated.
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.
Add ALLELES variable to --new_max_alleles help description.
IsolateInfo: Reset page variable.
Genome Comparator: Change 'truncated' to 'incomplete'.
Field help: Massively speed up scheme field display.
Use temp cache table that was developed for querying.
Show warning if seqbin not empty when uploading new sequences.
Typo.
Normalize Page::clean_locus arguments for memoization.
If clean_locus was called with different options for the same locus,
results could get mixed up.  Also, if a different memory address was
used for the arguemnt hashref memoization wouldn't occur anyway, since
the argument hashref would always be different even if the arguments
were the same.
Merge branch 'develop' into REST