S4 classes now in master branch

I was so enthusiastic about the newly discovered S4 classes and the smoothness with which they integrate with the C++ code (thanks to Rcpp), that I wrote a lot of code during my sons afternoon nap (mostly S4 versions of the existent functions). After some testing I decided to merge it back into master (not that dangerous as the number of users is still only me and my colleague). It works the same but the design is much more comprehensive and elegant.