Moved the warning about the cache not being on back into the constructor & simplified the construction method for the cache. If someone doesn't inherit from this correctly they'll loose the warning but that is all.

Ensembl core is now at v65. Patches to work with flat file handles in core like databases and supporting checksum derived xrefs

Replaced RefSeq_dna_predicted with Refseq_mRNA_predicted and RefSeq_ncRNA_predicted as the RefSeq_dna_predicted have been split for release 64.

Merging of UniParc mapping code into the Xref system. This relies on being able to contact the EBI based UniParc readonly database.

Brought in new_fast() as a speed increase.  Should probably consider moving new_fast() up to Storable.pm to give it to as many modules as possible & reduce code duplication

; TODO ; do_similarity_scoring      = 0
; TODO ; do_project_to_common_cs    = 0

Faster version of rearrange which ditches uc() and order modifying in favor of editing the input parameters directly with a tr///d. This is 35% faster than our original implementation. Test case suite has been run before this commit.

Caches are now created from an accessor rather than building them in the new(). This allows us to remove the new() and lets people inherit from here however they want to. It also stops us from auto-vivifying a plain hash which causes unintentional object retention.

clear_cache() did not de-reference the hash before clearning which could have caused the same situation of creating an auto-vivified hash.

Regression test put in place to stop this from happening again.