merge in changes from ensembl-64 for retrieving non-reference slices. Don't need to supply a value for logappend, verbose, interactive and dry_run parameters

Introduced Utils::IO namespace along with serializer code for GFF3 and human-readable formats. Pre-release, not intended for public use.
Also added Utils::BiotypeMapper that performs ontology mappings.

	formatting

	safe use of @aliases (don't expect registry to make copy of the list)

	quote argument names and values

Check the result of the print and die if we have an error. Bits of flatfiles have been missing so hopefully these will now be caught

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.

Edge case support for hive which allows for non-scheme URIs. We now treat these as if they are DB URIs.

Adding support for SQLite since the URI scheme does not take into account the fact that SQLite is a path and the concept of table does not play well with this

Minor POD corrections

Removing URIParser sub-package. It was nice in theory but I'd rather support different schemes using extensions to the URI package

Bringing in assertions for strand as well as for boolean types. Extending the test cases accordingly

Adding a more generic URI parser to replace the numerous places where people parse URIs in API code (mostly to get DB params)

bringing in /codon_start to represent offsets in the CDS based upon phase. The translation from phase to codon_start is non-obvious & has been documented.

fixes when identifying other stops -  1) ribosomal frameshift ignored, 2) stop codon being automatically annotated as a seleno and 3) non numerical values in comments