Added boundary class with the periodic subclass.
Made protected reaction variables private and accessible to subclasses
through functions instead. Removed some old optimization testing code.
Started working on describing general boundaries efficiently.
added boundary base class initialization functions and added config
fields.
Added mainsolver to boundary class. Made reaction mainsolver accessible
to subclasses.
Removed some silly old statements and comments which was periodicity
dependent. Much of the work is done already with regards to abstracting
the boundaries.