changes to provide multispecies support and also to use a unified command line processor (CliHelper)

fix for ChainedAssemblyMapper to map using the destination slice if one is provided http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-108

change to allow overriding of the default exonerate method for multiple sources with the same name http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-134

replaced methods ExonerateGappedBest1_agam and ExonerateGappedBest1_culex with ExonerateGappedBest1_55_perc_id

Added proper support for limiting the back-catalogue of patches that can be applied by --fix through the --oldest option.

Fixed PUBMED::culex_quinquefasciatus; added three plants species, setaria_italica solanum_lycopersicum oryza_brachyantha

Unbreaks bug where these options weren't used properly.

Do not quote identifiers if they are going into a prepared statement. Otherwise we end up with odd results

Returns default mappers from a class level. Makes serialisation using Storable possible without bringing in B::Deparse

Added support for 'Active finishing' contigs. Removed hack for HG1211_PATCH unknown orientation (although GRC have bot provided a solution as yet) BUT added in a new hack for contig FP700111.21 which had to be retrieved from SVA (current version is FP700111.23).