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.
Cleaning up ConfigIo and Fixed Simulation Restart

Removed ConfigIo::(readParameters|load|save|initialize) methods
because they are no longer needed since the CacheCapacity variables
are no longer necessary.  Fixed restarting bug due to PairPotential
class not saving and reloading the optional parameter nCellCut and
Simulation not re-allocating the distributor/collector objects on
load.
Work on SpCell and SpCellList in DdMd (not finished)
Merge pull request #27 from polymer1/sp

Distributor and Collector objects moved to Storage
Working on SpCellList (now compiles, but not testd).
Modified makefiles for Parallel Compilation

The makefiles have been modified to use the $(MAKE) variable instead of
the word make.  This allows the '-j N' flag to be passed to make which
tells it to spawn N processes and build in parallel. The following is
taken from the GNU make manual:

In order for make processes to communicate, the parent will pass
information to the child. Since this could result in problems if the
child process isn't actually a make, the parent will only do this if it
thinks the child is a make.
see http://www.gnu.org/software/make/manual/html_node/MAKE-Variable.html
Merge pull request #28 from polymer1/sp

Modified makefiles for Parallel Compilation
Merge branch 'devel' into sp
Editing SpSpecies and SpMolecule
Merge branch 'sp' into devel
Fixing bug in SpSpecies.cpp
Merge branch 'sp' into devel