Fixes for the alt alleles code. We needed to make sure we used the right variables in the code. Also needed to make sure an array is actually defined during construction

Fixing an issue raised by vega and non-standard DBAdaptor group names. Vega use ensembl to denote the ensembl db. We assumed incorrectly that core could always be used. That would always fail the moment a different group name was used

replaced ok tests with is where possible
replaced core test database with patch database

by farm3.

small queue for exonerate to finish.  Also added spaces after -R and -J
switches.

Making consistent through plants species the use of ncRNA_EG source for maintaining ncRNA genes xrefs asscoiated with logic_name ncrna_eg

ChEMBL xrefs are now being imported

- get_assembly_name
- get_assembly_date
- get_genebuild_start_date
- get_genebuild_method
- get_genebuild_initial_release_date
- get_genebuild_last_geneset_update

bug fixes for methods:
- get_toplevel
- get_karyotype
- get_coord_systems

returns a listref of all unique assembly versions available

will return a single string with the value of the default version of the assembly

replaced by GenomeContainer, hopefully more generic and in line with what already exists
presenting most of the generic features the assemblyadaptor add, but less REST only focused
will be further expanded with a genome table

This work allows for the hosting of more than one variation database (similar to
core-like databases such as rnaseq or otherfeatures). The Slice methods for core objects
allowed the specification of the database type. Variation methods now have the same
option. We have pushed much common logic into 4 methods to provide this automatic
defaulting behaviour.

We needed more methods to be able to handle alt allele group interactions. We also
needed to make sure a single gene could not be added more than once. Think we got
this one fixed