Given the shift to modules, it is not clear that the original include
directory structure is the best any more (with IMP/restraints holding
restraints, for example). I would propose that all public classes/
functions in the modules API be in headers in the module main include
directory. Structuring things this way means that the include paths
are the same as the namespace nesting which is the same as the python
module structure, which is nice. And the base classes are all together
in the include/IMP directory already.