Water built in its own function

Constructing the water mesh is now done in its own function as a
preparation for individual block faces to be added.
Removed unused imports
Changed accesses to "visited" array in Region.java to not use magic
numbers
Added some TODOs
Added Javadoc to Region.typeIsTransparent
Removed the commented out Region.writePOVStringOld()
Main.java does everything in the static main() function instead of the
constructor