undo accident shrinkage of the IMP caused by the new Mac tendency to save files automatically

git-svn-id: https://svn.salilab.org/imp/trunk@16297 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
just use boost.programoptions instead of gflags

it is easy enough to implement what we need and it removes a dependency. It also makes the api c++ class rather than macros, which is nice.

git-svn-id: https://svn.salilab.org/imp/trunk@16299 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing #include

git-svn-id: https://svn.salilab.org/imp/trunk@16300 e91f8c7b-0e32-4433-a9ac-4502d39a4eab