Patch submitted by Yuri Delia as aliases were added into the registry
even if a database was not found e.g. ontology. Additions moved
into the if blocks when we find and DB and constructed its adaptor.

Reverted Production DB dependency in order to allow Xref pipeline to run. Changes can be reinstated once slightly more mature.

stable_id_lookup is a separate public method
added archive_id_lookup method, which will look for the stable id in the archive_id_lookup table
the generic lookup method now calls stable_id_lookup
if no stable_id is found and $use_archive argument is given, the generic lookup will attempt to find the stable id
in the archive_id_lookup, ie amongst the retired ids
if a stable id is found using this, a 'retired' flag is returned as well

The method was called on the wrong object. Swithced around and tested

Nick in Ensembl Genomes has seen an issue with bacteria databases where
we exceed the number of connections on MySQL. As we loop through DBAdaptors
we do not disconnect. That means an ID which appears later on will have
opened all prior databases. The connection is still active. We now
disconnect this.

[ENSCORESW-478] and [ENSCORESW-467]. Brought in a Perl::Critic test being run on the lowest level. Tests are only run when we have the ENV TEST_AUTHOR is set to a true value. Otherwise it does not impact on the current test cases. Also had to fix a number of issues associcated with these flags. Mostly were due to not using warnings or strict. Anything I felt was ok or not my call has been annotated with a no critic flag.

Added a method that lists the species in available databases. Ancestral_ are ignored, and the list is filtered to a group type, defaulting to core dbs. Testcase is less than perfect, because the test db has so few species in it.

Make the verbose doc a bit more verbose. People in workshops could not find this method which points to poor documentation

[ENSCORESW-284]. Fixing registry lookups for compara gene trees. Also refactored it slightly; we will rip this out soon as we need a clearer separation.

[ENSCORESW-261]. Edits to allow for easier regulation adaptor creation. Grab the species name from the DB if it wasn't given to the adaptor and make sure we avoid returning the coord system core adaptor if the group was funcgen

Adding the no_alias check to the get_species_and_object_type() method to avoid warning about the lack of a lookup DB

load_registry_from_db - load the stable ids lookup database if found; get_species_and_object_type - use the stable id lookup database if found

load_XXXX() methods now return the number of adaptors which have appeared in the registry due to that method's invocation. This can be used to report success or failure to load databases.

Improving the error handling of the DBI connection in load_registry_from_db(). We now report an error if it cannot connect to the MySQL DB and if it was not pingable. Hopefully this catches both erronious scenarios.