small improvements to prepare-refseqs.pl
small improvements to prepare-refseqs.pl

rearrange the prepare-refseqs.pl code to put subroutines at the end,
make the no-refseqs condition be a warnings instead of an error, and
make sure the script exits with 0 when everything is fine

GMOD/jbrowse,SuLab/jbrowse,SuLab/jbrowse,erasche/jbrowse,erasche/jbrowse,SuLab/jbrowse,limeng12/jbrowse,erasche/jbrowse,limeng12/jbrowse,limeng12/jbrowse,GreggHelt2/apollo-test,GreggHelt2/apollo-test,limeng12/jbrowse,nathandunn/jbrowse,limeng12/jbrowse,SuLab/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,SuLab/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,Arabidopsis-Information-Portal/jbrowse,GMOD/jbrowse,erasche/jbrowse,Arabidopsis-Information-Portal/jbrowse,GreggHelt2/apollo-test,nathandunn/jbrowse,GMOD/jbrowse,limeng12/jbrowse,SuLab/jbrowse,erasche/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,nathandunn/jbrowse,Arabidopsis-Information-Portal/jbrowse,Arabidopsis-Information-Portal/jbrowse,SuLab/jbrowse,nathandunn/jbrowse,GreggHelt2/apollo-test,Arabidopsis-Information-Portal/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,limeng12/jbrowse,limeng12/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,GreggHelt2/apollo-test,erasche/jbrowse,GMOD/jbrowse,erasche/jbrowse,GMOD/jbrowse,GreggHelt2/apollo-test,Arabidopsis-Information-Portal/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,Arabidopsis-Information-Portal/jbrowse,igemsoftware/Shenzhen_BGIC_0101_2013,erasche/jbrowse,nathandunn/jbrowse,GreggHelt2/apollo-test,igemsoftware/Shenzhen_BGIC_0101_2013