suppress messages with external builds

git-svn-id: https://svn.salilab.org/imp/trunk@16564 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
be less tolerant of extra flags

git-svn-id: https://svn.salilab.org/imp/trunk@16565 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
better messages

git-svn-id: https://svn.salilab.org/imp/trunk@16566 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
make sure to skip disabled modules

git-svn-id: https://svn.salilab.org/imp/trunk@16567 e91f8c7b-0e32-4433-a9ac-4502d39a4eab