Preparing for move to R code

Initial commit. Not yet ready for production
Initial R files now in place

Initial files for R packaging are in place.
Comments! Lots of comments!

Added comments for R code. Modified R package files
Added header libraries and updated readme/makefile

include is not tracked in this commit
Changed eigen reordering to use vectorized ops.

Yep.
Merge branch 'R'
Merged R into master, fixed some small errors

Master is now primed for overlap algorithm