[IMP-dev] Index objects

After talking with Dina, I realized that there isn't really any circumstance under which it makes sense to use the ParticleIndex (or RestraintIndex) objects as one is always better off storing the Particle pointers. I propose removing the indexes and replacing the storage with a boost intrusive list. This will make it clear to new people that they should not be using the Indexes and make various code much simpler (since the range will always be full, even after deletions).

Likewise the ParticleIterators in model probably should be hidden so people aren't tempted to use them, but doing this is complicated by the macros being reused in many places and so is not as trivial a change.