Rewrite neighbor list code and other pieces so that there are no handles to internal data

[obrienpja]

Item 28 in Scott Meyers' Effective C++ says that C++ programmers should not return handles to object internals. I am currently using handles in this project, and I must remove them. The design I have implemented indeed feels wrong. I should try to rewrite this code in the way Scott describes in Item 28, and I should probably make sure the new design has the appropriate setters.