more updates to make certain things more explicit; tested & working with v1.1-rc3 process
more updates to make certain things more explicit; tested & working with v1.1-rc3 process

souravsingh/khmer,kdmurray91/khmer,Winterflower/khmer,Winterflower/khmer,ged-lab/khmer,F1000Research/khmer,ged-lab/khmer,jas14/khmer,F1000Research/khmer,kdmurray91/khmer,Winterflower/khmer,ged-lab/khmer,F1000Research/khmer,jas14/khmer,jas14/khmer,souravsingh/khmer,souravsingh/khmer,kdmurray91/khmer