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This reverts commit 3e24194c.

Fix for ENSCORESW-1816, bioperl's inconsistent handling of incomplete codons across versions. Trim any partial codons when translating unless told not to.

stable_id_version setter/getter for core object types, sets stable_id with a . delimited version or fetches stable_id with .version concatonated (if version is set)

if set, does not copy supporting_features between exons, resulting in a loss of information but speed up when storing numerous genes

corrected url for codon table

returns exon rank relative to an input transcript

if specified, will return sequence with lower cased UTRs

ENSCORESW-517: cdna2genomic returns 'genomic' coordinates which are relative to the slice of the feature
if the slice is not the whole chromosome, we need to adjust by adding the transcript->slice->start to the cdna2genomic return value, -1
if the slice is the whole chromosome, we add 1-1, so nothing changes
all test cases still pass with the modification

[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-445]. Fixes an issue with transformed and transfered transcripts. Attribute arrays are shallowed copied so attributes meant for the transformed object go back into the parent object. This causes more issues when you start to do multiple transformations from the same transcript. Regression test case added

[ENSCORESW-399] Fixing an issue reported from Steve Moss. We cause an exception because we do not check if we can project the cDNA location. Sometimes it is undefined.