add comments describing what the scripts do

git-svn-id: https://svn.salilab.org/imp/trunk@16648 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
better choice of default levels for checks

git-svn-id: https://svn.salilab.org/imp/trunk@16649 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
look at HAS_CHECKS rather than build type

git-svn-id: https://svn.salilab.org/imp/trunk@16650 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix index used

git-svn-id: https://svn.salilab.org/imp/trunk@16651 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
suppress runtime warning with model

git-svn-id: https://svn.salilab.org/imp/trunk@16652 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add usage check

git-svn-id: https://svn.salilab.org/imp/trunk@16653 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
update nup84 examples

git-svn-id: https://svn.salilab.org/imp/trunk@16654 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Attempt removal of hack that may not be needed any more.

git-svn-id: https://svn.salilab.org/imp/trunk@16655 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
suppress warnings

git-svn-id: https://svn.salilab.org/imp/trunk@16656 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
control warnings via pragmas rather than command line arguments to the compiler. This gives us much finer control and makes it so that they don't bleed out into other headers

git-svn-id: https://svn.salilab.org/imp/trunk@16657 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
undo vector relates hack to see if that fixes docs

git-svn-id: https://svn.salilab.org/imp/trunk@16658 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix handling of repeated cmake config calls

git-svn-id: https://svn.salilab.org/imp/trunk@16659 e91f8c7b-0e32-4433-a9ac-4502d39a4eab