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

Removed dependencies on non-core APIs.

Introduced two methods to translate to SO accessions and names.

This was missed off the first implementation of the table. It has resulted
in silly long query times because MySQL was forced into performing full
table scans to find evidence related to the transcript. Adding an index
in should fix this.

exception message.

times for writing.

second argument was being ignored

Added just a test for the new method filter_dir at the moment.

content of a directory.

corrupting multiple entries file.

Slice sequence is written into chunks (as specified by the chunk_factor
parameter given to the constructor) in method write_embl_seq, which now
returns the base counts.
Methods dump_embl has been modified accordingly. A template for a sequence
header is written, then the sequence, then we seek backwards to the
position of the sequence header to write it with the actual base counts
which have been figured out during the writing of the sequence.

Pros: memory efficiency
Cons: cannot dump to a file for which a compressed fh has been obtained,
      i.e. cannot call dump_embl method in a callback provided to
      Bio::EnsEMBL::Utils::IO::gz_work_with_file.

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

this works similarly to the stable_id_lookup table, but is populated with stable ids which are not current any more
the populate_stable_id_lookup.pl script has been updated to populate that table along with the other ones

updated test cases to check integrity of api once deprecated tables, columns and methods have been removed
test databases patched to schema 74