Modified $cs->equals to cope with DAS::CoordSystem

  When testing for existance of an object xref entry with
  linkage_annotation, treat NULLs as equals.

+ some formatting.

extra number (used by Ensembl Genomes) after the word "core", as in
"schizzosachromyces_pombe_core_0_51_1a".

Passes unit tests.

ignore_release arg added to gene store . It was set to 1 before but can now be passed, default is still set to 1

Removed empty line.

Removed trailing spaces.

tweaked AffyAlign
removed AlignAffyProbe & AlignAffy

firstEF added

description added for Uniprot_non_vertebrate

moved ENSEMBL_DB - > DATABASE_CORE and OTHER (non web user dbs) from ENSEMBL_{} -> DATABASE_, and changed the connection stuff to DATABASE_ as well

description for xrefs noew set to text rather than varchar(255) allowing longer descriptions, mainly for swissprot

get_all_DBAdaptors_by_connection():

  Arg [1]    : string, name of database
  Returntype : reference to list of DBAdaptors
  Exceptions : none
  Example    : @dba = @{ Bio::EnsEMBL::Registry
                  ->get_all_DBAdaptors_by_dbname($dbname) };
  Status     : Stable


Some formatting.

having DNA database and analysis database on separate servers:

  In new(), pick the coordinate system internal IDs from a
  CoordSystemAdaptor created from the DNA database (which may be located
  on another database server), then fetch the meta_coord data from the
  adaptor-local database using these.

Passes unit tests.