Modified the enum on object_xref from 72->73 patch c and the redump
re-did some data. Such as choosing a different encoding for some very
small values. All changes are small though.

now fully testing patches and haplotypes

allows testing on patches and similar

using current_schema_no_cvs everywhere now

The big post-merge alt allele commit. Changes to alt_allele table, new tests, and a couple of new objects.

currently not compatible with most existing tests

An option from the command-line (-current-schema-no-cvs) allows to load the
schema from the file system instead of fetching it from the CVS repository.

was not tested by PAR, as patches are stored on scaffolds, ie a different coord system

[ENSCORESW-499]. schemaPatches.t checks that the table.sql patch set matches what is in the patched database

[ENSCORESW-490]. Point raised by Dan. Default GFF3 for source is . not ensembl. Using . and supporting basic features

[ENSCORESW-490]. Fixing the GFF serializer which would add an additional ; at times and now supports a custom source field. Gene and transcript now both emit 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.

[ENSCORESW-479]. Making this module better at handling homologue Compara errors and also get it to die when you try to get homologues without a compara adaptor configured

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.