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.
Let's change the name of AtomDistributor::initialize(int) to AtomDistributor::allocate(int). I was inconsistent about name choices ("initialize" for distributors and "allocate" for collectors) and "allocate" is a more descriptive name. Please fix my mistake by renaming all the functions "allocate".