Workaround for “The total number of locks exceeds the lock table size” found when running xref pipeline

The only_tables options will now overwrite the tables in the target database even if these tables are newer on the target database. This is to replace the previous behaviour of copying to a different database and manually copying the MyISAM files to target database, this has caused issues in the past as the target database need to be flushed. The script automatically flush and optimize the target database. Please use this option with caution.

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Replaced dbh->{mysql_serverversion} with getting the MySQL version from the server variable. This seems to be more reliable

Set an object's default version to 1 when it is created,…

Move mysql_serverversion check the other way around as most of our servers are 5.6 or more recent. If mysql_serverversion is not defined then the script will run flush with read lock.

Removed checksum rsync flag for the update command line option. Checksum is too slow and make this option unusable

Remove $registry_register{_TYPE}

as it does not seem to be used anywhere. Furthermore, the same information
can be derived from $registry_register{_SPECIES}.

This piece of duplicated information take up a lot of spaces for a registry
with large number of species (e.g. ~600MB for Ensembl Bacteria at ~44k species).

Return all adaptors in the registry in get_all_DBAdaptors if no args …

Hope this time it works with differnt versions of Perl.

Also change file permissions back to 644.

Previously, when no args (either species or group) supplied, the implementation
at get_all_DBAdaptors requires looping through '_DBA' array and returns an array
of each DBA's reference. It takes long time if there are large number of DBAs
(e.g. >0.5s for ~88k DBAs).

This change returns the reference to the '_DBA' array itself directly in such cases.

Set an object's default version to 1 when it is created, rather than when it is stored, to allow undef versions (which can then be stored as NULLs in the database).