Index objects should use Doctrine's ArrayCollections for handling lists of related objects

[phenaproxima]

ArrayCollection is a fantastic array wrapper that will make it a bit easier to manipulate lists of related index objects (i.e., traits imported by a class, interfaces implemented, calls to a function, etc.). I suggest we use it. This will also add Doctrine\Common as a Pharborist dependency, although if we split the indexing stuff into its own component we could make it a dependency of just that component. Thoughts?