split input of seq_region files into seperate query/target seq_region files because the same names may be used on both sides

removed phase recalculation code, instead retain human phases which is the correct thing to do when exons are dropped

Modified store method slightly.  display_xref is now stored if set so update() does not need to be called as seperate step

Made global seq_region cache non-global.  Global cache for all dbs + mod_perl = very mysterious web bug.

In deprecated chr_name call, I've changed the code so it projects to the toplevel, not to the chromosome.  All species used to have chromosomes, so this always worked - the meaning of this call is now the same as it was, with the addded bonus that it works for species without chromosomes

Moved meta_coord table information retrieval/storage out of CoordSystemAdaptor and into new MetaCoordContainer class.  This was causing problems because the meta coord information should be stored/retrieved in the feature database and the coord system information should be stored/retrieved in the dna database

now gets protein_id vai previous dump's embl file; includes names, descriptions, Dros orhtologues; deals with bacterial genes; has comments

use a straight_join when joining to repeat_consensus on repeat_type, because the mysql query optimiser gets it wrong

removed fetch_all_by_Slice_and_type method, extended fetch_all_by_Slice method to take additional type arg