Fix parsing of genbank files containing CONTIG lines

In June of 2013 Refseq started allowing CONTIG and ORIGIN lines: http://lists.open-bio.org/pipermail/bioperl-l/2013-July/037427.html
This broke the bioperl genbank parser.
Although new releases of BioPerl have fixed this bug, we introduce a work around to remove these CONTIG lines before parsing with bioperl
Fix recently introduced bug where replicons would not be loaded
Add docs for INSTALL to not use MySQL strict mode