Bug fixes
Changes to vector_class and removed all traces of linked list.
Massive rewrite underway. This way be dragons.
More changes to code. Hopefully these will commit smoothly.
More code clean-up.
Split force loop into subroutines. Moved wrap out of simulation module.
Changed code to use one generic force loop. Only one super atype that has all information is now used.
libmdCode builds.
added libmdCode and a couple help scripts
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