Changes made to vertebrate resequencing update pipeline

These changes have been made to give us the option to override the MD5 value if it has changed, as well as provide a minimum run id for an update (since newer runs are analysed on different databases - we don't want to pull in all of the older ones too). As before, these 'features' are only accessed via specific flags set via the update_pipeline.pl script and have no effect on pipelines run without them!