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Converted the array containing atom block indices for the neighbor list from ushort2 to int.  This removes the hard limit of 2 million atoms.

Integrators control when atom reordering gets done, instead of having it happen automatically when forces are evaluated.  This simplifies some code, and also improves unintuitive behavior with CustomIntegrator.

Fixes a hard to catch bug when a boundingBoxSize increases in size in between a timestep, but does not trigger a rebuild of the neighbourlist. Affects the usage of singlePeriodicCopy in nonbonded force.  

When computing kinetic energy, make sure the shifted velocities are perpendicular to the constraints

Reduced memory use for random numbers, eliminated unnecessary calculation when generating random numbers

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Fixes uninitialized bits occurring in the PaddedNumAtoms regions by properly constructing them. This should hopefully get rid of some of the NaN errors we've been seeing.