cleaned out all references to raw neighborhood pointer.
Implemented new kick-ass function forAllNeighborsDo to replace
allNeighbor list. Works as a charm! Neighbor array removed and all tests
pass.
allReactions and activeReaction merged into "reactions", with new
forAllActiveReactionsDo function to take care of anything that might be
wanted done to all active reactions. Also then removed the functions for
updating reactions into activereactions array etc.
cleaned up tons of repetetive for loops. Both eases reading and
developing. All double declarations of neighbors and reactions are gone.
All tests pass.
merged branch cleanupPointers. 25% reduction in memory usage.