Added the opposite of slurp: spurt

Updated code dealing with flush to make sure that we don't flush source and target when noflush is turned on. Making sure to not flush target if noflushtarget is turned on

Allow translation start and stop to be defined within a transcript-level seq-edit

$species must be defined in Registry::add_DBAdaptor

bugfix: get_all_DBAdaptors() should always be returning an array-ref

If a fetched sub-sequence of an LRG doesn't fully encompass a sequence edit, the edit code didn't properly handle it.
There was also an off by one error in this situation.
Logic fixed to take in to account all start/end overlap combinations and tests added.
Jira ENSCORESW-2357

cosmetic changes

The update option should use checksum as it's the safest way to sync databases. Update alone is not enough and can lead to database corruption

- Added tests to cover UTR-coding sequence boundary for forward and reverse strands

Abandon MyISAM for xref pipeline. Core production server has too few resources devoted to InnoDB and the pipeline is failing at times.

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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