Improved usage docs.

Handles a karyotype containing non-existant chromosomes.  Warns, returns no bands for non-existant chr, but no longer dies deep in BaseFeatureAdaptor

changed an if defined to an if as 0 and '' shouldn't be considered true in that case

Renamed dump_xrefs to dump_core_xrefs to avoid conflict with similarly-named but differntly-functioning dump_xref

source_id removed from synonym,dependent_xref and primary_xref this information is available via the xref. linkage_source_id added to dependent xref. create_xrefs now also returns a hashref