pass along flags

git-svn-id: https://svn.salilab.org/imp/trunk@16638 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
mkdir on src dir so things can be put there easily

git-svn-id: https://svn.salilab.org/imp/trunk@16639 e91f8c7b-0e32-4433-a9ac-4502d39a4eab