[IMP-dev] Directory structure

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.