Changed deprecated method get_default_assembly() so that it actually works still, and changed deprecated warning

taken mostly from js5's lite scripts

fix: chimp karyotype features (if they even existed) would be on scaffolds since there are no chromosomes

'reconnect' is automatic when any access to the handle (db_handle, prepare)
is requested. Also added explicit connect method which returns if the
handle is already connected (shouldn't need to be called)

Reintroducing restrict_between_positions methods that was deleted when main trunk merge with new schema 20 core branch

now make sure to set up the group_id and level_id variables, but also the seqname is set without the need of having a slice associated. strands_reversed method set and returns 0 if variable undef

This is useful if you want to conserve db connections and use the same db for compara/pipeline etc.

No longer generates mapping paths with excessively complex shortest path algorithm