link .py bin files in setup_modules

git-svn-id: https://svn.salilab.org/imp/trunk@16590 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove unused files/dirs

git-svn-id: https://svn.salilab.org/imp/trunk@16591 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
don't ignore .os files as their being in the tree is a sign something is broken (which it is).

git-svn-id: https://svn.salilab.org/imp/trunk@16592 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
regularize structure of applications

Now nothing needs to be put into the SConscript files.

git-svn-id: https://svn.salilab.org/imp/trunk@16593 e91f8c7b-0e32-4433-a9ac-4502d39a4eab