Distributor and Collector objects moved to Storage

Restructured code so the (Atom|Group)(Distributor|Collector) objects are
now members of the (Atom|Group)Storage classes instead of the configIo
class.  This required doing the associating/initializing/allocating of
these objects only once inside the simulation class.  As a result of
this, specifying the parameters (atom|bond|angle|dihedral)CacheCapacity
inside the parameter file will no longer do anything.  These parameters
have all been hardcoded to 100.
Here also, please rename GroupDistributor<N>::initialize(int) as GroupDistributor<N>::allocate(int). This is what I should have called these functions in the first place.