include alternative sequences with correct start/end

[ENSCORESW-1038] Fix bug in negative stranded assembly exceptions. Scoped variables were forgetting their new values and coming back undef.

ignoring phase creates more false positives than false negatives
also improves the overall exon mapping

added transcript_biotype in attrib field

Convenience accessors in GeneAdaptor. Main code in BaseFeatureAdaptor. fetch_all_nearest_by_Feature provides an exhaustive mechanism for finding nearby features and ordering them by proximity.

Massive overhaul of fetch_all_nearest_by_feature to handle all crazy edge cases. More tests, correct tests, more docs.

Introduce Nathan's unit tests and notes.

do not run for these sources, existing xrefs will be kept as they are

seq returns N's if the slice is not in one of the default coord_systems

refseq_import should not be used

GFF3 export: unstranded features and using analysis.gff_source