removing deprecated/duplicated/unused scripts

switching to farm3 means that memory specification for bsub is in MB not KB i.e. -M and rusage need the same value

Ontology db updated to 73. Mouse ones updated as well but they do not really need it as it is not being rerun this release

Ok that was dumb. Do not under any circumstances add /xms to a regex that really depends on whitespace. Oddly enough it will not match anything

Slight change in logic. Do not skip a UniProt reecord because it is Ensembl derived annotation. Choose not to import the Gene Name into our system

- sub_Slice_same (does not weaken adaptor)
- seq_region_Slice_same (does not weaken adaptor)
- get_seq_region_id_same

This means that CoordSystem, DensityType, Map::Marker, Map::Ditag, Map::Qtl,
MiscSet, OntologyTerm and SeqRegionSynonym have now a fast constructor available.

Accordingly, new_fast is removed from Analysis, Feature, DataFile, DBEntry, RepeatConsensus,
Translation and UnmappedObject together with the import of weaken and isweak from
Scalar::Util.

Added error tolerance to cache copy in get_all_Transcripts. Major issue with original method returning undef instead of \[]. Not changed for legacy support.

currently not compatible with most existing tests

method to use is get_seq_region_id()

satisfies perl critic

Replaced all instantiations of pairs of circular slices with a call to the
above method.

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.

we do not want to retrieve all symlinks of the slice, just the slice itself

constructor of its parent (Storable) which is neglecting a lot of the UnmappedObject specific
attributes which instead are assigned and dealt with in the UnmappedObject constructor.
This hasn't been an issue so far as there doesn't seem to be any code calling this new_fast
implementation.

Improvements to documentation, describing the presence of forward and reverse strand features in the results of get_all_* methods.

newer and maintained versions are in ensembl-production checkout

Removed new_fast method already inherited from parent (Feature) class and after MiscFeatureAdaptor attribute default initialisation