clean up application include and add prelim modeller support

git-svn-id: https://svn.salilab.org/imp/trunk@16621 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add support for generated files within cmake

git-svn-id: https://svn.salilab.org/imp/trunk@16622 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add to history

git-svn-id: https://svn.salilab.org/imp/trunk@16623 e91f8c7b-0e32-4433-a9ac-4502d39a4eab